PLUMED-NEST

Project ID: plumID:21.030
Source: plumed-nest/nspe/plumed.dat
Originally used with PLUMED version: 2.4
Stable: zipped raw stdout - zipped raw stderr - stderr
Master: zipped raw stdout - zipped raw stderr - stderr

Click on the labels of the actions for more information on what each action computes

#! vim:ft=plumed

#RESTART 
#DEBUG logActivity FILE=debug.dat

ene: ENERGYCalculate the total potential energy of the simulation box. More details

The ENERGY action with label ene calculates somethingINCLUDEIncludes an external input file, similar to #include in C preprocessor. More details. Show included file FILEfile to be included=cn.dat
# The command:
# INCLUDE FILE=cn.dat
# ensures PLUMED loads the contents of the file called cn.dat
# The contents of this file are shown below (click the red comment to hide them).
#! vim:ft=plumed


# coordination 
The INCLUDE action with label cn.dat calculates somethingr1: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=13,22 #res 1 and 10 agg in trial 1
The COM action with label r1 calculates somethingr2: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=41,50
The COM action with label r2 calculates somethingr3: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=64,73
The COM action with label r3 calculates somethingr4: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=87,96
The COM action with label r4 calculates somethingr5: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=110,119
The COM action with label r5 calculates somethingr6: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=133,142 #res 6 and 9 should be coordinated in a helix
The COM action with label r6 calculates somethingr7: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=156,165
The COM action with label r7 calculates somethingr8: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=179,188
The COM action with label r8 calculates somethingr9: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=202,211 #CG-CH 
The COM action with label r9 calculates somethingr10: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=225,234
The COM action with label r10 calculates somethingr11: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=248,257
The COM action with label r11 calculates somethingr12: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=270,279

# coordination
The COM action with label r12 calculates somethingc: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=r1,r1,r1,r1,r1,r1,r1,r1,r1,r1,r1,r2,r2,r2,r2,r2,r2,r2,r2,r2,r2,r3,r3,r3,r3,r3,r3,r3,r3,r3,r4,r4,r4,r4,r4,r4,r4,r4,r5,r5,r5,r5,r5,r5,r5,r6,r6,r6,r6,r6,r6,r7,r7,r7,r7,r7,r8,r8,r8,r8,r9,r9,r9,r10,r10,r11  GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=r2,r3,r4,r5,r6,r7,r8,r9,r10,r11,r12,r3,r4,r5,r6,r7,r8,r9,r10,r11,r12,r4,r5,r6,r7,r8,r9,r10,r11,r12,r5,r6,r7,r8,r9,r10,r11,r12,r6,r7,r8,r9,r10,r11,r12,r7,r8,r9,r10,r11,r12,r8,r9,r10,r11,r12,r9,r10,r11,r12,r10,r11,r12,r11,r12,r12 R_0The r_0 parameter of the switching function=0.5 NN The n parameter of the switching function =8 MM The m parameter of the switching function; 0 implies 2*NN=12  NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=0.75 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=10 PAIR Pair only 1st element of the 1st group with 1st element in the second, etc

# each ring coord
The COORDINATION action with label c calculates the following quantities:
 Quantity   
 Description  
c.value
the value of the coordinationc1: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=r1 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=r2 R_0The r_0 parameter of the switching function=0.5 NN The n parameter of the switching function =8 MM The m parameter of the switching function; 0 implies 2*NN=12  NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=0.75 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=10 
The COORDINATION action with label c1 calculates the following quantities:
 Quantity   
 Description  
c1.value
the value of the coordinationc2: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=r1 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=r3 R_0The r_0 parameter of the switching function=0.5 NN The n parameter of the switching function =8 MM The m parameter of the switching function; 0 implies 2*NN=12  NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=0.75 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=10 
The COORDINATION action with label c2 calculates the following quantities:
 Quantity   
 Description  
c2.value
the value of the coordinationc3: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=r1 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=r4 R_0The r_0 parameter of the switching function=0.5 NN The n parameter of the switching function =8 MM The m parameter of the switching function; 0 implies 2*NN=12  NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=0.75 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=10 
The COORDINATION action with label c3 calculates the following quantities:
 Quantity   
 Description  
c3.value
the value of the coordinationc4: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=r1 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=r5 R_0The r_0 parameter of the switching function=0.5 NN The n parameter of the switching function =8 MM The m parameter of the switching function; 0 implies 2*NN=12  NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=0.75 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=10 
The COORDINATION action with label c4 calculates the following quantities:
 Quantity   
 Description  
c4.value
the value of the coordinationc5: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=r1 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=r6 R_0The r_0 parameter of the switching function=0.5 NN The n parameter of the switching function =8 MM The m parameter of the switching function; 0 implies 2*NN=12  NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=0.75 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=10 
The COORDINATION action with label c5 calculates the following quantities:
 Quantity   
 Description  
c5.value
the value of the coordinationc6: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=r1 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=r7 R_0The r_0 parameter of the switching function=0.5 NN The n parameter of the switching function =8 MM The m parameter of the switching function; 0 implies 2*NN=12  NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=0.75 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=10 
The COORDINATION action with label c6 calculates the following quantities:
 Quantity   
 Description  
c6.value
the value of the coordinationc7: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=r1 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=r8 R_0The r_0 parameter of the switching function=0.5 NN The n parameter of the switching function =8 MM The m parameter of the switching function; 0 implies 2*NN=12  NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=0.75 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=10 
The COORDINATION action with label c7 calculates the following quantities:
 Quantity   
 Description  
c7.value
the value of the coordinationc8: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=r1 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=r9 R_0The r_0 parameter of the switching function=0.5 NN The n parameter of the switching function =8 MM The m parameter of the switching function; 0 implies 2*NN=12  NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=0.75 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=10 
The COORDINATION action with label c8 calculates the following quantities:
 Quantity   
 Description  
c8.value
the value of the coordinationc9: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=r1 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=r10 R_0The r_0 parameter of the switching function=0.5 NN The n parameter of the switching function =8 MM The m parameter of the switching function; 0 implies 2*NN=12  NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=0.75 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=10 
The COORDINATION action with label c9 calculates the following quantities:
 Quantity   
 Description  
c9.value
the value of the coordinationc10: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=r1 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=r11 R_0The r_0 parameter of the switching function=0.5 NN The n parameter of the switching function =8 MM The m parameter of the switching function; 0 implies 2*NN=12  NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=0.75 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=10 
The COORDINATION action with label c10 calculates the following quantities:
 Quantity   
 Description  
c10.value
the value of the coordinationc11: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=r1 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=r12 R_0The r_0 parameter of the switching function=0.5 NN The n parameter of the switching function =8 MM The m parameter of the switching function; 0 implies 2*NN=12  NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=0.75 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=10 
The COORDINATION action with label c11 calculates the following quantities:
 Quantity   
 Description  
c11.value
the value of the coordinationc12: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=r2 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=r3 R_0The r_0 parameter of the switching function=0.5 NN The n parameter of the switching function =8 MM The m parameter of the switching function; 0 implies 2*NN=12  NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=0.75 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=10
The COORDINATION action with label c12 calculates the following quantities:
 Quantity   
 Description  
c12.value
the value of the coordinationc13: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=r2 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=r4 R_0The r_0 parameter of the switching function=0.5 NN The n parameter of the switching function =8 MM The m parameter of the switching function; 0 implies 2*NN=12  NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=0.75 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=10 
The COORDINATION action with label c13 calculates the following quantities:
 Quantity   
 Description  
c13.value
the value of the coordinationc14: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=r2 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=r5 R_0The r_0 parameter of the switching function=0.5 NN The n parameter of the switching function =8 MM The m parameter of the switching function; 0 implies 2*NN=12  NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=0.75 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=10 
The COORDINATION action with label c14 calculates the following quantities:
 Quantity   
 Description  
c14.value
the value of the coordinationc15: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=r2 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=r6 R_0The r_0 parameter of the switching function=0.5 NN The n parameter of the switching function =8 MM The m parameter of the switching function; 0 implies 2*NN=12  NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=0.75 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=10 
The COORDINATION action with label c15 calculates the following quantities:
 Quantity   
 Description  
c15.value
the value of the coordinationc16: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=r2 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=r7 R_0The r_0 parameter of the switching function=0.5 NN The n parameter of the switching function =8 MM The m parameter of the switching function; 0 implies 2*NN=12  NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=0.75 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=10 
The COORDINATION action with label c16 calculates the following quantities:
 Quantity   
 Description  
c16.value
the value of the coordinationc17: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=r2 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=r8 R_0The r_0 parameter of the switching function=0.5 NN The n parameter of the switching function =8 MM The m parameter of the switching function; 0 implies 2*NN=12  NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=0.75 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=10 
The COORDINATION action with label c17 calculates the following quantities:
 Quantity   
 Description  
c17.value
the value of the coordinationc18: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=r2 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=r9 R_0The r_0 parameter of the switching function=0.5 NN The n parameter of the switching function =8 MM The m parameter of the switching function; 0 implies 2*NN=12  NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=0.75 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=10 
The COORDINATION action with label c18 calculates the following quantities:
 Quantity   
 Description  
c18.value
the value of the coordinationc19: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=r2 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=r10 R_0The r_0 parameter of the switching function=0.5 NN The n parameter of the switching function =8 MM The m parameter of the switching function; 0 implies 2*NN=12  NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=0.75 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=10 
The COORDINATION action with label c19 calculates the following quantities:
 Quantity   
 Description  
c19.value
the value of the coordinationc20: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=r2 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=r11 R_0The r_0 parameter of the switching function=0.5 NN The n parameter of the switching function =8 MM The m parameter of the switching function; 0 implies 2*NN=12  NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=0.75 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=10 
The COORDINATION action with label c20 calculates the following quantities:
 Quantity   
 Description  
c20.value
the value of the coordinationc21: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=r2 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=r12 R_0The r_0 parameter of the switching function=0.5 NN The n parameter of the switching function =8 MM The m parameter of the switching function; 0 implies 2*NN=12  NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=0.75 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=10
The COORDINATION action with label c21 calculates the following quantities:
 Quantity   
 Description  
c21.value
the value of the coordinationc22: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=r3 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=r4 R_0The r_0 parameter of the switching function=0.5 NN The n parameter of the switching function =8 MM The m parameter of the switching function; 0 implies 2*NN=12  NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=0.75 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=10
The COORDINATION action with label c22 calculates the following quantities:
 Quantity   
 Description  
c22.value
the value of the coordinationc23: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=r3 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=r5 R_0The r_0 parameter of the switching function=0.5 NN The n parameter of the switching function =8 MM The m parameter of the switching function; 0 implies 2*NN=12  NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=0.75 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=10
The COORDINATION action with label c23 calculates the following quantities:
 Quantity   
 Description  
c23.value
the value of the coordinationc24: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=r3 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=r6 R_0The r_0 parameter of the switching function=0.5 NN The n parameter of the switching function =8 MM The m parameter of the switching function; 0 implies 2*NN=12  NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=0.75 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=10
The COORDINATION action with label c24 calculates the following quantities:
 Quantity   
 Description  
c24.value
the value of the coordinationc25: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=r3 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=r7 R_0The r_0 parameter of the switching function=0.5 NN The n parameter of the switching function =8 MM The m parameter of the switching function; 0 implies 2*NN=12  NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=0.75 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=10
The COORDINATION action with label c25 calculates the following quantities:
 Quantity   
 Description  
c25.value
the value of the coordinationc26: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=r3 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=r8 R_0The r_0 parameter of the switching function=0.5 NN The n parameter of the switching function =8 MM The m parameter of the switching function; 0 implies 2*NN=12  NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=0.75 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=10
The COORDINATION action with label c26 calculates the following quantities:
 Quantity   
 Description  
c26.value
the value of the coordinationc27: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=r3 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=r9 R_0The r_0 parameter of the switching function=0.5 NN The n parameter of the switching function =8 MM The m parameter of the switching function; 0 implies 2*NN=12  NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=0.75 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=10
The COORDINATION action with label c27 calculates the following quantities:
 Quantity   
 Description  
c27.value
the value of the coordinationc28: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=r3 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=r10 R_0The r_0 parameter of the switching function=0.5 NN The n parameter of the switching function =8 MM The m parameter of the switching function; 0 implies 2*NN=12  NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=0.75 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=10
The COORDINATION action with label c28 calculates the following quantities:
 Quantity   
 Description  
c28.value
the value of the coordinationc29: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=r3 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=r11 R_0The r_0 parameter of the switching function=0.5 NN The n parameter of the switching function =8 MM The m parameter of the switching function; 0 implies 2*NN=12  NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=0.75 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=10
The COORDINATION action with label c29 calculates the following quantities:
 Quantity   
 Description  
c29.value
the value of the coordinationc30: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=r3 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=r12 R_0The r_0 parameter of the switching function=0.5 NN The n parameter of the switching function =8 MM The m parameter of the switching function; 0 implies 2*NN=12  NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=0.75 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=10
The COORDINATION action with label c30 calculates the following quantities:
 Quantity   
 Description  
c30.value
the value of the coordinationc31: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=r4 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=r5 R_0The r_0 parameter of the switching function=0.5 NN The n parameter of the switching function =8 MM The m parameter of the switching function; 0 implies 2*NN=12  NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=0.75 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=10
The COORDINATION action with label c31 calculates the following quantities:
 Quantity   
 Description  
c31.value
the value of the coordinationc32: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=r4 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=r6 R_0The r_0 parameter of the switching function=0.5 NN The n parameter of the switching function =8 MM The m parameter of the switching function; 0 implies 2*NN=12  NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=0.75 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=10
The COORDINATION action with label c32 calculates the following quantities:
 Quantity   
 Description  
c32.value
the value of the coordinationc33: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=r4 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=r7 R_0The r_0 parameter of the switching function=0.5 NN The n parameter of the switching function =8 MM The m parameter of the switching function; 0 implies 2*NN=12  NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=0.75 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=10
The COORDINATION action with label c33 calculates the following quantities:
 Quantity   
 Description  
c33.value
the value of the coordinationc34: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=r4 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=r8 R_0The r_0 parameter of the switching function=0.5 NN The n parameter of the switching function =8 MM The m parameter of the switching function; 0 implies 2*NN=12  NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=0.75 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=10
The COORDINATION action with label c34 calculates the following quantities:
 Quantity   
 Description  
c34.value
the value of the coordinationc35: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=r4 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=r9 R_0The r_0 parameter of the switching function=0.5 NN The n parameter of the switching function =8 MM The m parameter of the switching function; 0 implies 2*NN=12  NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=0.75 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=10
The COORDINATION action with label c35 calculates the following quantities:
 Quantity   
 Description  
c35.value
the value of the coordinationc36: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=r4 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=r10 R_0The r_0 parameter of the switching function=0.5 NN The n parameter of the switching function =8 MM The m parameter of the switching function; 0 implies 2*NN=12  NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=0.75 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=10
The COORDINATION action with label c36 calculates the following quantities:
 Quantity   
 Description  
c36.value
the value of the coordinationc37: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=r4 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=r11 R_0The r_0 parameter of the switching function=0.5 NN The n parameter of the switching function =8 MM The m parameter of the switching function; 0 implies 2*NN=12  NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=0.75 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=10
The COORDINATION action with label c37 calculates the following quantities:
 Quantity   
 Description  
c37.value
the value of the coordinationc38: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=r4 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=r12 R_0The r_0 parameter of the switching function=0.5 NN The n parameter of the switching function =8 MM The m parameter of the switching function; 0 implies 2*NN=12  NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=0.75 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=10
The COORDINATION action with label c38 calculates the following quantities:
 Quantity   
 Description  
c38.value
the value of the coordinationc39: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=r5 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=r6 R_0The r_0 parameter of the switching function=0.5 NN The n parameter of the switching function =8 MM The m parameter of the switching function; 0 implies 2*NN=12  NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=0.75 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=10
The COORDINATION action with label c39 calculates the following quantities:
 Quantity   
 Description  
c39.value
the value of the coordinationc40: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=r5 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=r7 R_0The r_0 parameter of the switching function=0.5 NN The n parameter of the switching function =8 MM The m parameter of the switching function; 0 implies 2*NN=12  NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=0.75 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=10
The COORDINATION action with label c40 calculates the following quantities:
 Quantity   
 Description  
c40.value
the value of the coordinationc41: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=r5 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=r8 R_0The r_0 parameter of the switching function=0.5 NN The n parameter of the switching function =8 MM The m parameter of the switching function; 0 implies 2*NN=12  NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=0.75 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=10
The COORDINATION action with label c41 calculates the following quantities:
 Quantity   
 Description  
c41.value
the value of the coordinationc42: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=r5 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=r9 R_0The r_0 parameter of the switching function=0.5 NN The n parameter of the switching function =8 MM The m parameter of the switching function; 0 implies 2*NN=12  NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=0.75 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=10
The COORDINATION action with label c42 calculates the following quantities:
 Quantity   
 Description  
c42.value
the value of the coordinationc43: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=r5 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=r10 R_0The r_0 parameter of the switching function=0.5 NN The n parameter of the switching function =8 MM The m parameter of the switching function; 0 implies 2*NN=12  NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=0.75 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=10
The COORDINATION action with label c43 calculates the following quantities:
 Quantity   
 Description  
c43.value
the value of the coordinationc44: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=r5 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=r11 R_0The r_0 parameter of the switching function=0.5 NN The n parameter of the switching function =8 MM The m parameter of the switching function; 0 implies 2*NN=12  NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=0.75 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=10
The COORDINATION action with label c44 calculates the following quantities:
 Quantity   
 Description  
c44.value
the value of the coordinationc45: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=r5 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=r12 R_0The r_0 parameter of the switching function=0.5 NN The n parameter of the switching function =8 MM The m parameter of the switching function; 0 implies 2*NN=12  NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=0.75 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=10
The COORDINATION action with label c45 calculates the following quantities:
 Quantity   
 Description  
c45.value
the value of the coordinationc46: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=r6 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=r7 R_0The r_0 parameter of the switching function=0.5 NN The n parameter of the switching function =8 MM The m parameter of the switching function; 0 implies 2*NN=12  NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=0.75 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=10
The COORDINATION action with label c46 calculates the following quantities:
 Quantity   
 Description  
c46.value
the value of the coordinationc47: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=r6 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=r8 R_0The r_0 parameter of the switching function=0.5 NN The n parameter of the switching function =8 MM The m parameter of the switching function; 0 implies 2*NN=12  NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=0.75 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=10
The COORDINATION action with label c47 calculates the following quantities:
 Quantity   
 Description  
c47.value
the value of the coordinationc48: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=r6 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=r9 R_0The r_0 parameter of the switching function=0.5 NN The n parameter of the switching function =8 MM The m parameter of the switching function; 0 implies 2*NN=12  NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=0.75 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=10
The COORDINATION action with label c48 calculates the following quantities:
 Quantity   
 Description  
c48.value
the value of the coordinationc49: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=r6 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=r10 R_0The r_0 parameter of the switching function=0.5 NN The n parameter of the switching function =8 MM The m parameter of the switching function; 0 implies 2*NN=12  NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=0.75 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=10
The COORDINATION action with label c49 calculates the following quantities:
 Quantity   
 Description  
c49.value
the value of the coordinationc50: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=r6 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=r11 R_0The r_0 parameter of the switching function=0.5 NN The n parameter of the switching function =8 MM The m parameter of the switching function; 0 implies 2*NN=12  NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=0.75 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=10
The COORDINATION action with label c50 calculates the following quantities:
 Quantity   
 Description  
c50.value
the value of the coordinationc51: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=r6 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=r12 R_0The r_0 parameter of the switching function=0.5 NN The n parameter of the switching function =8 MM The m parameter of the switching function; 0 implies 2*NN=12  NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=0.75 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=10
The COORDINATION action with label c51 calculates the following quantities:
 Quantity   
 Description  
c51.value
the value of the coordinationc52: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=r7 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=r8 R_0The r_0 parameter of the switching function=0.5 NN The n parameter of the switching function =8 MM The m parameter of the switching function; 0 implies 2*NN=12  NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=0.75 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=10
The COORDINATION action with label c52 calculates the following quantities:
 Quantity   
 Description  
c52.value
the value of the coordinationc53: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=r7 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=r9 R_0The r_0 parameter of the switching function=0.5 NN The n parameter of the switching function =8 MM The m parameter of the switching function; 0 implies 2*NN=12  NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=0.75 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=10
The COORDINATION action with label c53 calculates the following quantities:
 Quantity   
 Description  
c53.value
the value of the coordinationc54: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=r7 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=r10 R_0The r_0 parameter of the switching function=0.5 NN The n parameter of the switching function =8 MM The m parameter of the switching function; 0 implies 2*NN=12  NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=0.75 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=10
The COORDINATION action with label c54 calculates the following quantities:
 Quantity   
 Description  
c54.value
the value of the coordinationc55: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=r7 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=r11 R_0The r_0 parameter of the switching function=0.5 NN The n parameter of the switching function =8 MM The m parameter of the switching function; 0 implies 2*NN=12  NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=0.75 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=10
The COORDINATION action with label c55 calculates the following quantities:
 Quantity   
 Description  
c55.value
the value of the coordinationc56: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=r7 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=r12 R_0The r_0 parameter of the switching function=0.5 NN The n parameter of the switching function =8 MM The m parameter of the switching function; 0 implies 2*NN=12  NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=0.75 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=10
The COORDINATION action with label c56 calculates the following quantities:
 Quantity   
 Description  
c56.value
the value of the coordinationc57: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=r8 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=r9 R_0The r_0 parameter of the switching function=0.5 NN The n parameter of the switching function =8 MM The m parameter of the switching function; 0 implies 2*NN=12  NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=0.75 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=10
The COORDINATION action with label c57 calculates the following quantities:
 Quantity   
 Description  
c57.value
the value of the coordinationc58: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=r8 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=r10 R_0The r_0 parameter of the switching function=0.5 NN The n parameter of the switching function =8 MM The m parameter of the switching function; 0 implies 2*NN=12  NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=0.75 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=10
The COORDINATION action with label c58 calculates the following quantities:
 Quantity   
 Description  
c58.value
the value of the coordinationc59: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=r8 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=r11 R_0The r_0 parameter of the switching function=0.5 NN The n parameter of the switching function =8 MM The m parameter of the switching function; 0 implies 2*NN=12  NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=0.75 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=10
The COORDINATION action with label c59 calculates the following quantities:
 Quantity   
 Description  
c59.value
the value of the coordinationc60: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=r8 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=r12 R_0The r_0 parameter of the switching function=0.5 NN The n parameter of the switching function =8 MM The m parameter of the switching function; 0 implies 2*NN=12  NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=0.75 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=10
The COORDINATION action with label c60 calculates the following quantities:
 Quantity   
 Description  
c60.value
the value of the coordinationc61: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=r9 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=r10 R_0The r_0 parameter of the switching function=0.5 NN The n parameter of the switching function =8 MM The m parameter of the switching function; 0 implies 2*NN=12  NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=0.75 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=10
The COORDINATION action with label c61 calculates the following quantities:
 Quantity   
 Description  
c61.value
the value of the coordinationc62: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=r9 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=r11 R_0The r_0 parameter of the switching function=0.5 NN The n parameter of the switching function =8 MM The m parameter of the switching function; 0 implies 2*NN=12  NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=0.75 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=10
The COORDINATION action with label c62 calculates the following quantities:
 Quantity   
 Description  
c62.value
the value of the coordinationc63: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=r9 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=r12 R_0The r_0 parameter of the switching function=0.5 NN The n parameter of the switching function =8 MM The m parameter of the switching function; 0 implies 2*NN=12  NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=0.75 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=10
The COORDINATION action with label c63 calculates the following quantities:
 Quantity   
 Description  
c63.value
the value of the coordinationc64: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=r10 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=r11 R_0The r_0 parameter of the switching function=0.5 NN The n parameter of the switching function =8 MM The m parameter of the switching function; 0 implies 2*NN=12  NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=0.75 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=10
The COORDINATION action with label c64 calculates the following quantities:
 Quantity   
 Description  
c64.value
the value of the coordinationc65: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=r10 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=r12 R_0The r_0 parameter of the switching function=0.5 NN The n parameter of the switching function =8 MM The m parameter of the switching function; 0 implies 2*NN=12  NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=0.75 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=10
The COORDINATION action with label c65 calculates the following quantities:
 Quantity   
 Description  
c65.value
the value of the coordinationc66: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=r11 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=r12 R_0The r_0 parameter of the switching function=0.5 NN The n parameter of the switching function =8 MM The m parameter of the switching function; 0 implies 2*NN=12  NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=0.75 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=10

# --- End of included input --- The COORDINATION action with label c66 calculates the following quantities:
 Quantity   
 Description  
c66.value
the value of the coordinationINCLUDEIncludes an external input file, similar to #include in C preprocessor. More details. Show included file FILEfile to be included=cv.dat
# The command:
# INCLUDE FILE=cv.dat
# ensures PLUMED loads the contents of the file called cv.dat
# The contents of this file are shown below (click the red comment to hide them).
#! vim:ft=plumed

#RESTART 

# COLVARS 

# rg
The INCLUDE action with label cv.dat calculates somethingrg: GYRATIONCalculate the radius of gyration, or other properties related to it. More details TYPE The type of calculation relative to the Gyration Tensor you want to perform=RADIUS ATOMSthe group of atoms that you are calculating the Gyration Tensor for=1,3,4,29,31,32,52,54,55,75,77,78,98,100,101,121,123,124,144,146,147,167,169,170,190,192,193,213,215,216,236,238,239,259,261

# dihedrals 
# phi 
The GYRATION action with label rg calculates the following quantities:
 Quantity   
 Description  
rg.value
the radius that was computed from the weightsphi0: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=24,4,3,1
The TORSION action with label phi0 calculates the following quantities:
 Quantity   
 Description  
phi0.value
the TORSION involving these atomsphi1: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=1,32,31,29
The TORSION action with label phi1 calculates the following quantities:
 Quantity   
 Description  
phi1.value
the TORSION involving these atomsphi2: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=29,55,54,52
The TORSION action with label phi2 calculates the following quantities:
 Quantity   
 Description  
phi2.value
the TORSION involving these atomsphi3: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=52,78,77,75
The TORSION action with label phi3 calculates the following quantities:
 Quantity   
 Description  
phi3.value
the TORSION involving these atomsphi4: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=75,101,100,98
The TORSION action with label phi4 calculates the following quantities:
 Quantity   
 Description  
phi4.value
the TORSION involving these atomsphi5: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=98,124,123,121
The TORSION action with label phi5 calculates the following quantities:
 Quantity   
 Description  
phi5.value
the TORSION involving these atomsphi6: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=121,147,146,144
The TORSION action with label phi6 calculates the following quantities:
 Quantity   
 Description  
phi6.value
the TORSION involving these atomsphi7: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=144,170,169,167
The TORSION action with label phi7 calculates the following quantities:
 Quantity   
 Description  
phi7.value
the TORSION involving these atomsphi8: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=167,193,192,190
The TORSION action with label phi8 calculates the following quantities:
 Quantity   
 Description  
phi8.value
the TORSION involving these atomsphi9: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=190,216,215,213
The TORSION action with label phi9 calculates the following quantities:
 Quantity   
 Description  
phi9.value
the TORSION involving these atomsphi10: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=213,239,238,236

# psi 
The TORSION action with label phi10 calculates the following quantities:
 Quantity   
 Description  
phi10.value
the TORSION involving these atomspsi0: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=26,24,4,3
The TORSION action with label psi0 calculates the following quantities:
 Quantity   
 Description  
psi0.value
the TORSION involving these atomspsi1: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=3,1,32,31
The TORSION action with label psi1 calculates the following quantities:
 Quantity   
 Description  
psi1.value
the TORSION involving these atomspsi2: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=31,29,55,54
The TORSION action with label psi2 calculates the following quantities:
 Quantity   
 Description  
psi2.value
the TORSION involving these atomspsi3: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=54,52,78,77
The TORSION action with label psi3 calculates the following quantities:
 Quantity   
 Description  
psi3.value
the TORSION involving these atomspsi4: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=77,75,101,100
The TORSION action with label psi4 calculates the following quantities:
 Quantity   
 Description  
psi4.value
the TORSION involving these atomspsi5: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=100,98,124,123
The TORSION action with label psi5 calculates the following quantities:
 Quantity   
 Description  
psi5.value
the TORSION involving these atomspsi6: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=123,121,147,146
The TORSION action with label psi6 calculates the following quantities:
 Quantity   
 Description  
psi6.value
the TORSION involving these atomspsi7: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=146,144,170,169
The TORSION action with label psi7 calculates the following quantities:
 Quantity   
 Description  
psi7.value
the TORSION involving these atomspsi8: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=169,167,193,192
The TORSION action with label psi8 calculates the following quantities:
 Quantity   
 Description  
psi8.value
the TORSION involving these atomspsi9: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=192,190,216,215
The TORSION action with label psi9 calculates the following quantities:
 Quantity   
 Description  
psi9.value
the TORSION involving these atomspsi10: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=215,213,239,238
The TORSION action with label psi10 calculates the following quantities:
 Quantity   
 Description  
psi10.value
the TORSION involving these atomspsi11: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=238,236,261,259

# omega 
The TORSION action with label psi11 calculates the following quantities:
 Quantity   
 Description  
psi11.value
the TORSION involving these atomsomega0: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=4,3,1,32
The TORSION action with label omega0 calculates the following quantities:
 Quantity   
 Description  
omega0.value
the TORSION involving these atomsomega1: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=32,31,29,55
The TORSION action with label omega1 calculates the following quantities:
 Quantity   
 Description  
omega1.value
the TORSION involving these atomsomega2: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=55,54,52,78
The TORSION action with label omega2 calculates the following quantities:
 Quantity   
 Description  
omega2.value
the TORSION involving these atomsomega3: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=78,77,75,101
The TORSION action with label omega3 calculates the following quantities:
 Quantity   
 Description  
omega3.value
the TORSION involving these atomsomega4: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=101,100,98,124
The TORSION action with label omega4 calculates the following quantities:
 Quantity   
 Description  
omega4.value
the TORSION involving these atomsomega5: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=124,123,121,147
The TORSION action with label omega5 calculates the following quantities:
 Quantity   
 Description  
omega5.value
the TORSION involving these atomsomega6: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=147,146,144,170
The TORSION action with label omega6 calculates the following quantities:
 Quantity   
 Description  
omega6.value
the TORSION involving these atomsomega7: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=170,169,167,193
The TORSION action with label omega7 calculates the following quantities:
 Quantity   
 Description  
omega7.value
the TORSION involving these atomsomega8: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=193,192,190,216
The TORSION action with label omega8 calculates the following quantities:
 Quantity   
 Description  
omega8.value
the TORSION involving these atomsomega9: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=216,215,213,239
The TORSION action with label omega9 calculates the following quantities:
 Quantity   
 Description  
omega9.value
the TORSION involving these atomsomega10: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=239,238,236,261

# chi-1
The TORSION action with label omega10 calculates the following quantities:
 Quantity   
 Description  
omega10.value
the TORSION involving these atomschi0: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=4,3,7,9
The TORSION action with label chi0 calculates the following quantities:
 Quantity   
 Description  
chi0.value
the TORSION involving these atomschi1: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=32,31,35,37
The TORSION action with label chi1 calculates the following quantities:
 Quantity   
 Description  
chi1.value
the TORSION involving these atomschi2: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=55,54,58,60
The TORSION action with label chi2 calculates the following quantities:
 Quantity   
 Description  
chi2.value
the TORSION involving these atomschi3: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=78,77,81,83
The TORSION action with label chi3 calculates the following quantities:
 Quantity   
 Description  
chi3.value
the TORSION involving these atomschi4: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=101,100,104,106
The TORSION action with label chi4 calculates the following quantities:
 Quantity   
 Description  
chi4.value
the TORSION involving these atomschi5: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=124,123,127,129
The TORSION action with label chi5 calculates the following quantities:
 Quantity   
 Description  
chi5.value
the TORSION involving these atomschi6: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=147,146,150,152
The TORSION action with label chi6 calculates the following quantities:
 Quantity   
 Description  
chi6.value
the TORSION involving these atomschi7: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=170,169,173,175
The TORSION action with label chi7 calculates the following quantities:
 Quantity   
 Description  
chi7.value
the TORSION involving these atomschi8: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=193,192,196,198
The TORSION action with label chi8 calculates the following quantities:
 Quantity   
 Description  
chi8.value
the TORSION involving these atomschi9: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=216,215,219,221
The TORSION action with label chi9 calculates the following quantities:
 Quantity   
 Description  
chi9.value
the TORSION involving these atomschi10: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=239,238,242,244
The TORSION action with label chi10 calculates the following quantities:
 Quantity   
 Description  
chi10.value
the TORSION involving these atomschi11: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=261,259,264,266

# chi-2
The TORSION action with label chi11 calculates the following quantities:
 Quantity   
 Description  
chi11.value
the TORSION involving these atomschi20: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=3,7,13,14
The TORSION action with label chi20 calculates the following quantities:
 Quantity   
 Description  
chi20.value
the TORSION involving these atomschi21: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=31,35,41,42
The TORSION action with label chi21 calculates the following quantities:
 Quantity   
 Description  
chi21.value
the TORSION involving these atomschi22: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=54,58,64,65
The TORSION action with label chi22 calculates the following quantities:
 Quantity   
 Description  
chi22.value
the TORSION involving these atomschi23: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=77,81,87,88
The TORSION action with label chi23 calculates the following quantities:
 Quantity   
 Description  
chi23.value
the TORSION involving these atomschi24: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=100,104,110,111
The TORSION action with label chi24 calculates the following quantities:
 Quantity   
 Description  
chi24.value
the TORSION involving these atomschi25: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=123,127,133,134
The TORSION action with label chi25 calculates the following quantities:
 Quantity   
 Description  
chi25.value
the TORSION involving these atomschi26: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=146,150,156,157
The TORSION action with label chi26 calculates the following quantities:
 Quantity   
 Description  
chi26.value
the TORSION involving these atomschi27: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=169,173,179,180
The TORSION action with label chi27 calculates the following quantities:
 Quantity   
 Description  
chi27.value
the TORSION involving these atomschi28: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=192,196,202,203
The TORSION action with label chi28 calculates the following quantities:
 Quantity   
 Description  
chi28.value
the TORSION involving these atomschi29: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=215,219,225,226
The TORSION action with label chi29 calculates the following quantities:
 Quantity   
 Description  
chi29.value
the TORSION involving these atomschi210: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=238,242,248,249
The TORSION action with label chi210 calculates the following quantities:
 Quantity   
 Description  
chi210.value
the TORSION involving these atomschi211: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=259,264,270,271

# --- End of included input --- The TORSION action with label chi211 calculates the following quantities:
 Quantity   
 Description  
chi211.value
the TORSION involving these atomsINCLUDEIncludes an external input file, similar to #include in C preprocessor. More details. Show included file FILEfile to be included=ab.dat
# The command:
# INCLUDE FILE=ab.dat
# ensures PLUMED loads the contents of the file called ab.dat
# The contents of this file are shown below (click the red comment to hide them).
#! vim:ft=plumed

#alphaD- cis
The INCLUDE action with label ab.dat calculates somethingALPHABETAMeasures a distance including pbc between the instantaneous values of a set of torsional angles and set of reference values. More details ...
ATOMS1the atoms involved for each of the torsions you wish to calculate=24,4,3,1 REFERENCE1the reference values for each of the torsional angles=-1.57
ATOMS2the atoms involved for each of the torsions you wish to calculate=1,32,31,29 REFERENCE2the reference values for each of the torsional angles=-1.57
ATOMS3the atoms involved for each of the torsions you wish to calculate=29,55,54,52 REFERENCE3the reference values for each of the torsional angles=-1.57
ATOMS4the atoms involved for each of the torsions you wish to calculate=52,78,77,75 REFERENCE4the reference values for each of the torsional angles=-1.57
ATOMS5the atoms involved for each of the torsions you wish to calculate=75,101,100,98 REFERENCE5the reference values for each of the torsional angles=-1.57
ATOMS6the atoms involved for each of the torsions you wish to calculate=98,124,123,121 REFERENCE6the reference values for each of the torsional angles=-1.57
ATOMS7the atoms involved for each of the torsions you wish to calculate=121,147,146,144 REFERENCE7the reference values for each of the torsional angles=-1.57
ATOMS8the atoms involved for each of the torsions you wish to calculate=144,170,169,167 REFERENCE8the reference values for each of the torsional angles=-1.57
ATOMS9the atoms involved for each of the torsions you wish to calculate=167,193,192,190 REFERENCE9the reference values for each of the torsional angles=-1.57
ATOMS10the atoms involved for each of the torsions you wish to calculate=190,216,215,213 REFERENCE10the reference values for each of the torsional angles=-1.57
ATOMS11the atoms involved for each of the torsions you wish to calculate=213,239,238,236 REFERENCE11the reference values for each of the torsional angles=-1.57
ATOMS12the atoms involved for each of the torsions you wish to calculate=26,24,4,3 REFERENCE12the reference values for each of the torsional angles=3.14
ATOMS13the atoms involved for each of the torsions you wish to calculate=3,1,32,31 REFERENCE13the reference values for each of the torsional angles=3.14
ATOMS14the atoms involved for each of the torsions you wish to calculate=31,29,55,54 REFERENCE14the reference values for each of the torsional angles=3.14
ATOMS15the atoms involved for each of the torsions you wish to calculate=54,52,78,77 REFERENCE15the reference values for each of the torsional angles=3.14
ATOMS16the atoms involved for each of the torsions you wish to calculate=77,75,101,100 REFERENCE16the reference values for each of the torsional angles=3.14
ATOMS17the atoms involved for each of the torsions you wish to calculate=100,98,124,123 REFERENCE17the reference values for each of the torsional angles=3.14
ATOMS18the atoms involved for each of the torsions you wish to calculate=123,121,147,146 REFERENCE18the reference values for each of the torsional angles=3.14
ATOMS19the atoms involved for each of the torsions you wish to calculate=146,144,170,169 REFERENCE19the reference values for each of the torsional angles=3.14
ATOMS20the atoms involved for each of the torsions you wish to calculate=169,167,193,192 REFERENCE20the reference values for each of the torsional angles=3.14
ATOMS21the atoms involved for each of the torsions you wish to calculate=192,190,216,215 REFERENCE21the reference values for each of the torsional angles=3.14
ATOMS22the atoms involved for each of the torsions you wish to calculate=215,213,239,238 REFERENCE22the reference values for each of the torsional angles=3.14
ATOMS23the atoms involved for each of the torsions you wish to calculate=238,236,261,259 REFERENCE23the reference values for each of the torsional angles=3.14
ATOMS24the atoms involved for each of the torsions you wish to calculate=4,3,1,32 REFERENCE24the reference values for each of the torsional angles=0
ATOMS25the atoms involved for each of the torsions you wish to calculate=32,31,29,55 REFERENCE25the reference values for each of the torsional angles=0
ATOMS26the atoms involved for each of the torsions you wish to calculate=55,54,52,78 REFERENCE26the reference values for each of the torsional angles=0
ATOMS27the atoms involved for each of the torsions you wish to calculate=78,77,75,101 REFERENCE27the reference values for each of the torsional angles=0
ATOMS28the atoms involved for each of the torsions you wish to calculate=101,100,98,124 REFERENCE28the reference values for each of the torsional angles=0
ATOMS29the atoms involved for each of the torsions you wish to calculate=124,123,121,147 REFERENCE29the reference values for each of the torsional angles=0
ATOMS30the atoms involved for each of the torsions you wish to calculate=147,146,144,170 REFERENCE30the reference values for each of the torsional angles=0
ATOMS31the atoms involved for each of the torsions you wish to calculate=170,169,167,193 REFERENCE31the reference values for each of the torsional angles=0
ATOMS32the atoms involved for each of the torsions you wish to calculate=193,192,190,216 REFERENCE32the reference values for each of the torsional angles=0
ATOMS33the atoms involved for each of the torsions you wish to calculate=216,215,213,239 REFERENCE33the reference values for each of the torsional angles=0
ATOMS34the atoms involved for each of the torsions you wish to calculate=239,238,236,261 REFERENCE34the reference values for each of the torsional angles=0
LABELa label for the action so that its output can be referenced in the input to other actions=alpha_d_minus
... ALPHABETA

#alphaD- trans
The ALPHABETA action with label alpha_d_minus calculates the following quantities:
 Quantity   
 Description  
alpha_d_minus.value
the alpha beta CVALPHABETAMeasures a distance including pbc between the instantaneous values of a set of torsional angles and set of reference values. More details ...
ATOMS1the atoms involved for each of the torsions you wish to calculate=24,4,3,1 REFERENCE1the reference values for each of the torsional angles=-1.57
ATOMS2the atoms involved for each of the torsions you wish to calculate=1,32,31,29 REFERENCE2the reference values for each of the torsional angles=-1.57
ATOMS3the atoms involved for each of the torsions you wish to calculate=29,55,54,52 REFERENCE3the reference values for each of the torsional angles=-1.57
ATOMS4the atoms involved for each of the torsions you wish to calculate=52,78,77,75 REFERENCE4the reference values for each of the torsional angles=-1.57
ATOMS5the atoms involved for each of the torsions you wish to calculate=75,101,100,98 REFERENCE5the reference values for each of the torsional angles=-1.57
ATOMS6the atoms involved for each of the torsions you wish to calculate=98,124,123,121 REFERENCE6the reference values for each of the torsional angles=-1.57
ATOMS7the atoms involved for each of the torsions you wish to calculate=121,147,146,144 REFERENCE7the reference values for each of the torsional angles=-1.57
ATOMS8the atoms involved for each of the torsions you wish to calculate=144,170,169,167 REFERENCE8the reference values for each of the torsional angles=-1.57
ATOMS9the atoms involved for each of the torsions you wish to calculate=167,193,192,190 REFERENCE9the reference values for each of the torsional angles=-1.57
ATOMS10the atoms involved for each of the torsions you wish to calculate=190,216,215,213 REFERENCE10the reference values for each of the torsional angles=-1.57
ATOMS11the atoms involved for each of the torsions you wish to calculate=213,239,238,236 REFERENCE11the reference values for each of the torsional angles=-1.57
ATOMS12the atoms involved for each of the torsions you wish to calculate=26,24,4,3 REFERENCE12the reference values for each of the torsional angles=3.14
ATOMS13the atoms involved for each of the torsions you wish to calculate=3,1,32,31 REFERENCE13the reference values for each of the torsional angles=3.14
ATOMS14the atoms involved for each of the torsions you wish to calculate=31,29,55,54 REFERENCE14the reference values for each of the torsional angles=3.14
ATOMS15the atoms involved for each of the torsions you wish to calculate=54,52,78,77 REFERENCE15the reference values for each of the torsional angles=3.14
ATOMS16the atoms involved for each of the torsions you wish to calculate=77,75,101,100 REFERENCE16the reference values for each of the torsional angles=3.14
ATOMS17the atoms involved for each of the torsions you wish to calculate=100,98,124,123 REFERENCE17the reference values for each of the torsional angles=3.14
ATOMS18the atoms involved for each of the torsions you wish to calculate=123,121,147,146 REFERENCE18the reference values for each of the torsional angles=3.14
ATOMS19the atoms involved for each of the torsions you wish to calculate=146,144,170,169 REFERENCE19the reference values for each of the torsional angles=3.14
ATOMS20the atoms involved for each of the torsions you wish to calculate=169,167,193,192 REFERENCE20the reference values for each of the torsional angles=3.14
ATOMS21the atoms involved for each of the torsions you wish to calculate=192,190,216,215 REFERENCE21the reference values for each of the torsional angles=3.14
ATOMS22the atoms involved for each of the torsions you wish to calculate=215,213,239,238 REFERENCE22the reference values for each of the torsional angles=3.14
ATOMS23the atoms involved for each of the torsions you wish to calculate=238,236,261,259 REFERENCE23the reference values for each of the torsional angles=3.14
ATOMS24the atoms involved for each of the torsions you wish to calculate=4,3,1,32 REFERENCE24the reference values for each of the torsional angles=3.14
ATOMS25the atoms involved for each of the torsions you wish to calculate=32,31,29,55 REFERENCE25the reference values for each of the torsional angles=3.14
ATOMS26the atoms involved for each of the torsions you wish to calculate=55,54,52,78 REFERENCE26the reference values for each of the torsional angles=3.14
ATOMS27the atoms involved for each of the torsions you wish to calculate=78,77,75,101 REFERENCE27the reference values for each of the torsional angles=3.14
ATOMS28the atoms involved for each of the torsions you wish to calculate=101,100,98,124 REFERENCE28the reference values for each of the torsional angles=3.14
ATOMS29the atoms involved for each of the torsions you wish to calculate=124,123,121,147 REFERENCE29the reference values for each of the torsional angles=3.14
ATOMS30the atoms involved for each of the torsions you wish to calculate=147,146,144,170 REFERENCE30the reference values for each of the torsional angles=3.14
ATOMS31the atoms involved for each of the torsions you wish to calculate=170,169,167,193 REFERENCE31the reference values for each of the torsional angles=3.14
ATOMS32the atoms involved for each of the torsions you wish to calculate=193,192,190,216 REFERENCE32the reference values for each of the torsional angles=3.14
ATOMS33the atoms involved for each of the torsions you wish to calculate=216,215,213,239 REFERENCE33the reference values for each of the torsional angles=3.14
ATOMS34the atoms involved for each of the torsions you wish to calculate=239,238,236,261 REFERENCE34the reference values for each of the torsional angles=3.14
LABELa label for the action so that its output can be referenced in the input to other actions=alpha_d_minus_trans
... ALPHABETA

#alphaD+ cis
The ALPHABETA action with label alpha_d_minus_trans calculates the following quantities:
 Quantity   
 Description  
alpha_d_minus_trans.value
the alpha beta CVALPHABETAMeasures a distance including pbc between the instantaneous values of a set of torsional angles and set of reference values. More details ...
ATOMS1the atoms involved for each of the torsions you wish to calculate=24,4,3,1 REFERENCE1the reference values for each of the torsional angles=1.57
ATOMS2the atoms involved for each of the torsions you wish to calculate=1,32,31,29 REFERENCE2the reference values for each of the torsional angles=1.57
ATOMS3the atoms involved for each of the torsions you wish to calculate=29,55,54,52 REFERENCE3the reference values for each of the torsional angles=1.57
ATOMS4the atoms involved for each of the torsions you wish to calculate=52,78,77,75 REFERENCE4the reference values for each of the torsional angles=1.57
ATOMS5the atoms involved for each of the torsions you wish to calculate=75,101,100,98 REFERENCE5the reference values for each of the torsional angles=1.57
ATOMS6the atoms involved for each of the torsions you wish to calculate=98,124,123,121 REFERENCE6the reference values for each of the torsional angles=1.57
ATOMS7the atoms involved for each of the torsions you wish to calculate=121,147,146,144 REFERENCE7the reference values for each of the torsional angles=1.57
ATOMS8the atoms involved for each of the torsions you wish to calculate=144,170,169,167 REFERENCE8the reference values for each of the torsional angles=1.57
ATOMS9the atoms involved for each of the torsions you wish to calculate=167,193,192,190 REFERENCE9the reference values for each of the torsional angles=1.57
ATOMS10the atoms involved for each of the torsions you wish to calculate=190,216,215,213 REFERENCE10the reference values for each of the torsional angles=1.57
ATOMS11the atoms involved for each of the torsions you wish to calculate=213,239,238,236 REFERENCE11the reference values for each of the torsional angles=1.57
ATOMS12the atoms involved for each of the torsions you wish to calculate=26,24,4,3 REFERENCE12the reference values for each of the torsional angles=3.14
ATOMS13the atoms involved for each of the torsions you wish to calculate=3,1,32,31 REFERENCE13the reference values for each of the torsional angles=3.14
ATOMS14the atoms involved for each of the torsions you wish to calculate=31,29,55,54 REFERENCE14the reference values for each of the torsional angles=3.14
ATOMS15the atoms involved for each of the torsions you wish to calculate=54,52,78,77 REFERENCE15the reference values for each of the torsional angles=3.14
ATOMS16the atoms involved for each of the torsions you wish to calculate=77,75,101,100 REFERENCE16the reference values for each of the torsional angles=3.14
ATOMS17the atoms involved for each of the torsions you wish to calculate=100,98,124,123 REFERENCE17the reference values for each of the torsional angles=3.14
ATOMS18the atoms involved for each of the torsions you wish to calculate=123,121,147,146 REFERENCE18the reference values for each of the torsional angles=3.14
ATOMS19the atoms involved for each of the torsions you wish to calculate=146,144,170,169 REFERENCE19the reference values for each of the torsional angles=3.14
ATOMS20the atoms involved for each of the torsions you wish to calculate=169,167,193,192 REFERENCE20the reference values for each of the torsional angles=3.14
ATOMS21the atoms involved for each of the torsions you wish to calculate=192,190,216,215 REFERENCE21the reference values for each of the torsional angles=3.14
ATOMS22the atoms involved for each of the torsions you wish to calculate=215,213,239,238 REFERENCE22the reference values for each of the torsional angles=3.14
ATOMS23the atoms involved for each of the torsions you wish to calculate=238,236,261,259 REFERENCE23the reference values for each of the torsional angles=3.14
ATOMS24the atoms involved for each of the torsions you wish to calculate=4,3,1,32 REFERENCE24the reference values for each of the torsional angles=0
ATOMS25the atoms involved for each of the torsions you wish to calculate=32,31,29,55 REFERENCE25the reference values for each of the torsional angles=0
ATOMS26the atoms involved for each of the torsions you wish to calculate=55,54,52,78 REFERENCE26the reference values for each of the torsional angles=0
ATOMS27the atoms involved for each of the torsions you wish to calculate=78,77,75,101 REFERENCE27the reference values for each of the torsional angles=0
ATOMS28the atoms involved for each of the torsions you wish to calculate=101,100,98,124 REFERENCE28the reference values for each of the torsional angles=0
ATOMS29the atoms involved for each of the torsions you wish to calculate=124,123,121,147 REFERENCE29the reference values for each of the torsional angles=0
ATOMS30the atoms involved for each of the torsions you wish to calculate=147,146,144,170 REFERENCE30the reference values for each of the torsional angles=0
ATOMS31the atoms involved for each of the torsions you wish to calculate=170,169,167,193 REFERENCE31the reference values for each of the torsional angles=0
ATOMS32the atoms involved for each of the torsions you wish to calculate=193,192,190,216 REFERENCE32the reference values for each of the torsional angles=0
ATOMS33the atoms involved for each of the torsions you wish to calculate=216,215,213,239 REFERENCE33the reference values for each of the torsional angles=0
ATOMS34the atoms involved for each of the torsions you wish to calculate=239,238,236,261 REFERENCE34the reference values for each of the torsional angles=0
LABELa label for the action so that its output can be referenced in the input to other actions=alpha_d_plus
... ALPHABETA

#alphaD+ trans
The ALPHABETA action with label alpha_d_plus calculates the following quantities:
 Quantity   
 Description  
alpha_d_plus.value
the alpha beta CVALPHABETAMeasures a distance including pbc between the instantaneous values of a set of torsional angles and set of reference values. More details ...
ATOMS1the atoms involved for each of the torsions you wish to calculate=24,4,3,1 REFERENCE1the reference values for each of the torsional angles=1.57
ATOMS2the atoms involved for each of the torsions you wish to calculate=1,32,31,29 REFERENCE2the reference values for each of the torsional angles=1.57
ATOMS3the atoms involved for each of the torsions you wish to calculate=29,55,54,52 REFERENCE3the reference values for each of the torsional angles=1.57
ATOMS4the atoms involved for each of the torsions you wish to calculate=52,78,77,75 REFERENCE4the reference values for each of the torsional angles=1.57
ATOMS5the atoms involved for each of the torsions you wish to calculate=75,101,100,98 REFERENCE5the reference values for each of the torsional angles=1.57
ATOMS6the atoms involved for each of the torsions you wish to calculate=98,124,123,121 REFERENCE6the reference values for each of the torsional angles=1.57
ATOMS7the atoms involved for each of the torsions you wish to calculate=121,147,146,144 REFERENCE7the reference values for each of the torsional angles=1.57
ATOMS8the atoms involved for each of the torsions you wish to calculate=144,170,169,167 REFERENCE8the reference values for each of the torsional angles=1.57
ATOMS9the atoms involved for each of the torsions you wish to calculate=167,193,192,190 REFERENCE9the reference values for each of the torsional angles=1.57
ATOMS10the atoms involved for each of the torsions you wish to calculate=190,216,215,213 REFERENCE10the reference values for each of the torsional angles=1.57
ATOMS11the atoms involved for each of the torsions you wish to calculate=213,239,238,236 REFERENCE11the reference values for each of the torsional angles=1.57
ATOMS12the atoms involved for each of the torsions you wish to calculate=26,24,4,3 REFERENCE12the reference values for each of the torsional angles=3.14
ATOMS13the atoms involved for each of the torsions you wish to calculate=3,1,32,31 REFERENCE13the reference values for each of the torsional angles=3.14
ATOMS14the atoms involved for each of the torsions you wish to calculate=31,29,55,54 REFERENCE14the reference values for each of the torsional angles=3.14
ATOMS15the atoms involved for each of the torsions you wish to calculate=54,52,78,77 REFERENCE15the reference values for each of the torsional angles=3.14
ATOMS16the atoms involved for each of the torsions you wish to calculate=77,75,101,100 REFERENCE16the reference values for each of the torsional angles=3.14
ATOMS17the atoms involved for each of the torsions you wish to calculate=100,98,124,123 REFERENCE17the reference values for each of the torsional angles=3.14
ATOMS18the atoms involved for each of the torsions you wish to calculate=123,121,147,146 REFERENCE18the reference values for each of the torsional angles=3.14
ATOMS19the atoms involved for each of the torsions you wish to calculate=146,144,170,169 REFERENCE19the reference values for each of the torsional angles=3.14
ATOMS20the atoms involved for each of the torsions you wish to calculate=169,167,193,192 REFERENCE20the reference values for each of the torsional angles=3.14
ATOMS21the atoms involved for each of the torsions you wish to calculate=192,190,216,215 REFERENCE21the reference values for each of the torsional angles=3.14
ATOMS22the atoms involved for each of the torsions you wish to calculate=215,213,239,238 REFERENCE22the reference values for each of the torsional angles=3.14
ATOMS23the atoms involved for each of the torsions you wish to calculate=238,236,261,259 REFERENCE23the reference values for each of the torsional angles=3.14
ATOMS24the atoms involved for each of the torsions you wish to calculate=4,3,1,32 REFERENCE24the reference values for each of the torsional angles=3.14
ATOMS25the atoms involved for each of the torsions you wish to calculate=32,31,29,55 REFERENCE25the reference values for each of the torsional angles=3.14
ATOMS26the atoms involved for each of the torsions you wish to calculate=55,54,52,78 REFERENCE26the reference values for each of the torsional angles=3.14
ATOMS27the atoms involved for each of the torsions you wish to calculate=78,77,75,101 REFERENCE27the reference values for each of the torsional angles=3.14
ATOMS28the atoms involved for each of the torsions you wish to calculate=101,100,98,124 REFERENCE28the reference values for each of the torsional angles=3.14
ATOMS29the atoms involved for each of the torsions you wish to calculate=124,123,121,147 REFERENCE29the reference values for each of the torsional angles=3.14
ATOMS30the atoms involved for each of the torsions you wish to calculate=147,146,144,170 REFERENCE30the reference values for each of the torsional angles=3.14
ATOMS31the atoms involved for each of the torsions you wish to calculate=170,169,167,193 REFERENCE31the reference values for each of the torsional angles=3.14
ATOMS32the atoms involved for each of the torsions you wish to calculate=193,192,190,216 REFERENCE32the reference values for each of the torsional angles=3.14
ATOMS33the atoms involved for each of the torsions you wish to calculate=216,215,213,239 REFERENCE33the reference values for each of the torsional angles=3.14
ATOMS34the atoms involved for each of the torsions you wish to calculate=239,238,236,261 REFERENCE34the reference values for each of the torsional angles=3.14
LABELa label for the action so that its output can be referenced in the input to other actions=alpha_d_plus_trans
... ALPHABETA

# alpha+ cis
The ALPHABETA action with label alpha_d_plus_trans calculates the following quantities:
 Quantity   
 Description  
alpha_d_plus_trans.value
the alpha beta CVALPHABETAMeasures a distance including pbc between the instantaneous values of a set of torsional angles and set of reference values. More details ...
ATOMS1the atoms involved for each of the torsions you wish to calculate=24,4,3,1 REFERENCE1the reference values for each of the torsional angles=0.87
ATOMS2the atoms involved for each of the torsions you wish to calculate=1,32,31,29 REFERENCE2the reference values for each of the torsional angles=0.87
ATOMS3the atoms involved for each of the torsions you wish to calculate=29,55,54,52 REFERENCE3the reference values for each of the torsional angles=0.87
ATOMS4the atoms involved for each of the torsions you wish to calculate=52,78,77,75 REFERENCE4the reference values for each of the torsional angles=0.87
ATOMS5the atoms involved for each of the torsions you wish to calculate=75,101,100,98 REFERENCE5the reference values for each of the torsional angles=0.87
ATOMS6the atoms involved for each of the torsions you wish to calculate=98,124,123,121 REFERENCE6the reference values for each of the torsional angles=0.87
ATOMS7the atoms involved for each of the torsions you wish to calculate=121,147,146,144 REFERENCE7the reference values for each of the torsional angles=0.87
ATOMS8the atoms involved for each of the torsions you wish to calculate=144,170,169,167 REFERENCE8the reference values for each of the torsional angles=0.87
ATOMS9the atoms involved for each of the torsions you wish to calculate=167,193,192,190 REFERENCE9the reference values for each of the torsional angles=0.87
ATOMS10the atoms involved for each of the torsions you wish to calculate=190,216,215,213 REFERENCE10the reference values for each of the torsional angles=0.87
ATOMS11the atoms involved for each of the torsions you wish to calculate=213,239,238,236 REFERENCE11the reference values for each of the torsional angles=0.87
ATOMS12the atoms involved for each of the torsions you wish to calculate=26,24,4,3 REFERENCE12the reference values for each of the torsional angles=1.0
ATOMS13the atoms involved for each of the torsions you wish to calculate=3,1,32,31 REFERENCE13the reference values for each of the torsional angles=1.0
ATOMS14the atoms involved for each of the torsions you wish to calculate=31,29,55,54 REFERENCE14the reference values for each of the torsional angles=1.0
ATOMS15the atoms involved for each of the torsions you wish to calculate=54,52,78,77 REFERENCE15the reference values for each of the torsional angles=1.0
ATOMS16the atoms involved for each of the torsions you wish to calculate=77,75,101,100 REFERENCE16the reference values for each of the torsional angles=1.0
ATOMS17the atoms involved for each of the torsions you wish to calculate=100,98,124,123 REFERENCE17the reference values for each of the torsional angles=1.0
ATOMS18the atoms involved for each of the torsions you wish to calculate=123,121,147,146 REFERENCE18the reference values for each of the torsional angles=1.0
ATOMS19the atoms involved for each of the torsions you wish to calculate=146,144,170,169 REFERENCE19the reference values for each of the torsional angles=1.0
ATOMS20the atoms involved for each of the torsions you wish to calculate=169,167,193,192 REFERENCE20the reference values for each of the torsional angles=1.0
ATOMS21the atoms involved for each of the torsions you wish to calculate=192,190,216,215 REFERENCE21the reference values for each of the torsional angles=1.0
ATOMS22the atoms involved for each of the torsions you wish to calculate=215,213,239,238 REFERENCE22the reference values for each of the torsional angles=1.0
ATOMS23the atoms involved for each of the torsions you wish to calculate=238,236,261,259 REFERENCE23the reference values for each of the torsional angles=1.0
ATOMS24the atoms involved for each of the torsions you wish to calculate=4,3,1,32 REFERENCE24the reference values for each of the torsional angles=0
ATOMS25the atoms involved for each of the torsions you wish to calculate=32,31,29,55 REFERENCE25the reference values for each of the torsional angles=0
ATOMS26the atoms involved for each of the torsions you wish to calculate=55,54,52,78 REFERENCE26the reference values for each of the torsional angles=0
ATOMS27the atoms involved for each of the torsions you wish to calculate=78,77,75,101 REFERENCE27the reference values for each of the torsional angles=0
ATOMS28the atoms involved for each of the torsions you wish to calculate=101,100,98,124 REFERENCE28the reference values for each of the torsional angles=0
ATOMS29the atoms involved for each of the torsions you wish to calculate=124,123,121,147 REFERENCE29the reference values for each of the torsional angles=0
ATOMS30the atoms involved for each of the torsions you wish to calculate=147,146,144,170 REFERENCE30the reference values for each of the torsional angles=0
ATOMS31the atoms involved for each of the torsions you wish to calculate=170,169,167,193 REFERENCE31the reference values for each of the torsional angles=0
ATOMS32the atoms involved for each of the torsions you wish to calculate=193,192,190,216 REFERENCE32the reference values for each of the torsional angles=0
ATOMS33the atoms involved for each of the torsions you wish to calculate=216,215,213,239 REFERENCE33the reference values for each of the torsional angles=0
ATOMS34the atoms involved for each of the torsions you wish to calculate=239,238,236,261 REFERENCE34the reference values for each of the torsional angles=0
LABELa label for the action so that its output can be referenced in the input to other actions=alpha_plus
... ALPHABETA

# alpha+ trans
The ALPHABETA action with label alpha_plus calculates the following quantities:
 Quantity   
 Description  
alpha_plus.value
the alpha beta CVALPHABETAMeasures a distance including pbc between the instantaneous values of a set of torsional angles and set of reference values. More details ...
ATOMS1the atoms involved for each of the torsions you wish to calculate=24,4,3,1 REFERENCE1the reference values for each of the torsional angles=0.87
ATOMS2the atoms involved for each of the torsions you wish to calculate=1,32,31,29 REFERENCE2the reference values for each of the torsional angles=0.87
ATOMS3the atoms involved for each of the torsions you wish to calculate=29,55,54,52 REFERENCE3the reference values for each of the torsional angles=0.87
ATOMS4the atoms involved for each of the torsions you wish to calculate=52,78,77,75 REFERENCE4the reference values for each of the torsional angles=0.87
ATOMS5the atoms involved for each of the torsions you wish to calculate=75,101,100,98 REFERENCE5the reference values for each of the torsional angles=0.87
ATOMS6the atoms involved for each of the torsions you wish to calculate=98,124,123,121 REFERENCE6the reference values for each of the torsional angles=0.87
ATOMS7the atoms involved for each of the torsions you wish to calculate=121,147,146,144 REFERENCE7the reference values for each of the torsional angles=0.87
ATOMS8the atoms involved for each of the torsions you wish to calculate=144,170,169,167 REFERENCE8the reference values for each of the torsional angles=0.87
ATOMS9the atoms involved for each of the torsions you wish to calculate=167,193,192,190 REFERENCE9the reference values for each of the torsional angles=0.87
ATOMS10the atoms involved for each of the torsions you wish to calculate=190,216,215,213 REFERENCE10the reference values for each of the torsional angles=0.87
ATOMS11the atoms involved for each of the torsions you wish to calculate=213,239,238,236 REFERENCE11the reference values for each of the torsional angles=0.87
ATOMS12the atoms involved for each of the torsions you wish to calculate=26,24,4,3 REFERENCE12the reference values for each of the torsional angles=1.0
ATOMS13the atoms involved for each of the torsions you wish to calculate=3,1,32,31 REFERENCE13the reference values for each of the torsional angles=1.0
ATOMS14the atoms involved for each of the torsions you wish to calculate=31,29,55,54 REFERENCE14the reference values for each of the torsional angles=1.0
ATOMS15the atoms involved for each of the torsions you wish to calculate=54,52,78,77 REFERENCE15the reference values for each of the torsional angles=1.0
ATOMS16the atoms involved for each of the torsions you wish to calculate=77,75,101,100 REFERENCE16the reference values for each of the torsional angles=1.0
ATOMS17the atoms involved for each of the torsions you wish to calculate=100,98,124,123 REFERENCE17the reference values for each of the torsional angles=1.0
ATOMS18the atoms involved for each of the torsions you wish to calculate=123,121,147,146 REFERENCE18the reference values for each of the torsional angles=1.0
ATOMS19the atoms involved for each of the torsions you wish to calculate=146,144,170,169 REFERENCE19the reference values for each of the torsional angles=1.0
ATOMS20the atoms involved for each of the torsions you wish to calculate=169,167,193,192 REFERENCE20the reference values for each of the torsional angles=1.0
ATOMS21the atoms involved for each of the torsions you wish to calculate=192,190,216,215 REFERENCE21the reference values for each of the torsional angles=1.0
ATOMS22the atoms involved for each of the torsions you wish to calculate=215,213,239,238 REFERENCE22the reference values for each of the torsional angles=1.0
ATOMS23the atoms involved for each of the torsions you wish to calculate=238,236,261,259 REFERENCE23the reference values for each of the torsional angles=1.0
ATOMS24the atoms involved for each of the torsions you wish to calculate=4,3,1,32 REFERENCE24the reference values for each of the torsional angles=3.14
ATOMS25the atoms involved for each of the torsions you wish to calculate=32,31,29,55 REFERENCE25the reference values for each of the torsional angles=3.14
ATOMS26the atoms involved for each of the torsions you wish to calculate=55,54,52,78 REFERENCE26the reference values for each of the torsional angles=3.14
ATOMS27the atoms involved for each of the torsions you wish to calculate=78,77,75,101 REFERENCE27the reference values for each of the torsional angles=3.14
ATOMS28the atoms involved for each of the torsions you wish to calculate=101,100,98,124 REFERENCE28the reference values for each of the torsional angles=3.14
ATOMS29the atoms involved for each of the torsions you wish to calculate=124,123,121,147 REFERENCE29the reference values for each of the torsional angles=3.14
ATOMS30the atoms involved for each of the torsions you wish to calculate=147,146,144,170 REFERENCE30the reference values for each of the torsional angles=3.14
ATOMS31the atoms involved for each of the torsions you wish to calculate=170,169,167,193 REFERENCE31the reference values for each of the torsional angles=3.14
ATOMS32the atoms involved for each of the torsions you wish to calculate=193,192,190,216 REFERENCE32the reference values for each of the torsional angles=3.14
ATOMS33the atoms involved for each of the torsions you wish to calculate=216,215,213,239 REFERENCE33the reference values for each of the torsional angles=3.14
ATOMS34the atoms involved for each of the torsions you wish to calculate=239,238,236,261 REFERENCE34the reference values for each of the torsional angles=3.14
LABELa label for the action so that its output can be referenced in the input to other actions=alpha_plus_trans
... ALPHABETA

# alpha- cis
The ALPHABETA action with label alpha_plus_trans calculates the following quantities:
 Quantity   
 Description  
alpha_plus_trans.value
the alpha beta CVALPHABETAMeasures a distance including pbc between the instantaneous values of a set of torsional angles and set of reference values. More details ...
ATOMS1the atoms involved for each of the torsions you wish to calculate=24,4,3,1 REFERENCE1the reference values for each of the torsional angles=-0.87
ATOMS2the atoms involved for each of the torsions you wish to calculate=1,32,31,29 REFERENCE2the reference values for each of the torsional angles=-0.87
ATOMS3the atoms involved for each of the torsions you wish to calculate=29,55,54,52 REFERENCE3the reference values for each of the torsional angles=-0.87
ATOMS4the atoms involved for each of the torsions you wish to calculate=52,78,77,75 REFERENCE4the reference values for each of the torsional angles=-0.87
ATOMS5the atoms involved for each of the torsions you wish to calculate=75,101,100,98 REFERENCE5the reference values for each of the torsional angles=-0.87
ATOMS6the atoms involved for each of the torsions you wish to calculate=98,124,123,121 REFERENCE6the reference values for each of the torsional angles=-0.87
ATOMS7the atoms involved for each of the torsions you wish to calculate=121,147,146,144 REFERENCE7the reference values for each of the torsional angles=-0.87
ATOMS8the atoms involved for each of the torsions you wish to calculate=144,170,169,167 REFERENCE8the reference values for each of the torsional angles=-0.87
ATOMS9the atoms involved for each of the torsions you wish to calculate=167,193,192,190 REFERENCE9the reference values for each of the torsional angles=-0.87
ATOMS10the atoms involved for each of the torsions you wish to calculate=190,216,215,213 REFERENCE10the reference values for each of the torsional angles=-0.87
ATOMS11the atoms involved for each of the torsions you wish to calculate=213,239,238,236 REFERENCE11the reference values for each of the torsional angles=-0.87
ATOMS12the atoms involved for each of the torsions you wish to calculate=26,24,4,3 REFERENCE12the reference values for each of the torsional angles=-1.0
ATOMS13the atoms involved for each of the torsions you wish to calculate=3,1,32,31 REFERENCE13the reference values for each of the torsional angles=-1.0
ATOMS14the atoms involved for each of the torsions you wish to calculate=31,29,55,54 REFERENCE14the reference values for each of the torsional angles=-1.0
ATOMS15the atoms involved for each of the torsions you wish to calculate=54,52,78,77 REFERENCE15the reference values for each of the torsional angles=-1.0
ATOMS16the atoms involved for each of the torsions you wish to calculate=77,75,101,100 REFERENCE16the reference values for each of the torsional angles=-1.0
ATOMS17the atoms involved for each of the torsions you wish to calculate=100,98,124,123 REFERENCE17the reference values for each of the torsional angles=-1.0
ATOMS18the atoms involved for each of the torsions you wish to calculate=123,121,147,146 REFERENCE18the reference values for each of the torsional angles=-1.0
ATOMS19the atoms involved for each of the torsions you wish to calculate=146,144,170,169 REFERENCE19the reference values for each of the torsional angles=-1.0
ATOMS20the atoms involved for each of the torsions you wish to calculate=169,167,193,192 REFERENCE20the reference values for each of the torsional angles=-1.0
ATOMS21the atoms involved for each of the torsions you wish to calculate=192,190,216,215 REFERENCE21the reference values for each of the torsional angles=-1.0
ATOMS22the atoms involved for each of the torsions you wish to calculate=215,213,239,238 REFERENCE22the reference values for each of the torsional angles=-1.0
ATOMS23the atoms involved for each of the torsions you wish to calculate=238,236,261,259 REFERENCE23the reference values for each of the torsional angles=-1.0
ATOMS24the atoms involved for each of the torsions you wish to calculate=4,3,1,32 REFERENCE24the reference values for each of the torsional angles=0
ATOMS25the atoms involved for each of the torsions you wish to calculate=32,31,29,55 REFERENCE25the reference values for each of the torsional angles=0
ATOMS26the atoms involved for each of the torsions you wish to calculate=55,54,52,78 REFERENCE26the reference values for each of the torsional angles=0
ATOMS27the atoms involved for each of the torsions you wish to calculate=78,77,75,101 REFERENCE27the reference values for each of the torsional angles=0
ATOMS28the atoms involved for each of the torsions you wish to calculate=101,100,98,124 REFERENCE28the reference values for each of the torsional angles=0
ATOMS29the atoms involved for each of the torsions you wish to calculate=124,123,121,147 REFERENCE29the reference values for each of the torsional angles=0
ATOMS30the atoms involved for each of the torsions you wish to calculate=147,146,144,170 REFERENCE30the reference values for each of the torsional angles=0
ATOMS31the atoms involved for each of the torsions you wish to calculate=170,169,167,193 REFERENCE31the reference values for each of the torsional angles=0
ATOMS32the atoms involved for each of the torsions you wish to calculate=193,192,190,216 REFERENCE32the reference values for each of the torsional angles=0
ATOMS33the atoms involved for each of the torsions you wish to calculate=216,215,213,239 REFERENCE33the reference values for each of the torsional angles=0
ATOMS34the atoms involved for each of the torsions you wish to calculate=239,238,236,261 REFERENCE34the reference values for each of the torsional angles=0
LABELa label for the action so that its output can be referenced in the input to other actions=alpha_minus
... ALPHABETA

# alpha- trans
The ALPHABETA action with label alpha_minus calculates the following quantities:
 Quantity   
 Description  
alpha_minus.value
the alpha beta CVALPHABETAMeasures a distance including pbc between the instantaneous values of a set of torsional angles and set of reference values. More details ...
ATOMS1the atoms involved for each of the torsions you wish to calculate=24,4,3,1 REFERENCE1the reference values for each of the torsional angles=-0.87
ATOMS2the atoms involved for each of the torsions you wish to calculate=1,32,31,29 REFERENCE2the reference values for each of the torsional angles=-0.87
ATOMS3the atoms involved for each of the torsions you wish to calculate=29,55,54,52 REFERENCE3the reference values for each of the torsional angles=-0.87
ATOMS4the atoms involved for each of the torsions you wish to calculate=52,78,77,75 REFERENCE4the reference values for each of the torsional angles=-0.87
ATOMS5the atoms involved for each of the torsions you wish to calculate=75,101,100,98 REFERENCE5the reference values for each of the torsional angles=-0.87
ATOMS6the atoms involved for each of the torsions you wish to calculate=98,124,123,121 REFERENCE6the reference values for each of the torsional angles=-0.87
ATOMS7the atoms involved for each of the torsions you wish to calculate=121,147,146,144 REFERENCE7the reference values for each of the torsional angles=-0.87
ATOMS8the atoms involved for each of the torsions you wish to calculate=144,170,169,167 REFERENCE8the reference values for each of the torsional angles=-0.87
ATOMS9the atoms involved for each of the torsions you wish to calculate=167,193,192,190 REFERENCE9the reference values for each of the torsional angles=-0.87
ATOMS10the atoms involved for each of the torsions you wish to calculate=190,216,215,213 REFERENCE10the reference values for each of the torsional angles=-0.87
ATOMS11the atoms involved for each of the torsions you wish to calculate=213,239,238,236 REFERENCE11the reference values for each of the torsional angles=-0.87
ATOMS12the atoms involved for each of the torsions you wish to calculate=26,24,4,3 REFERENCE12the reference values for each of the torsional angles=-1.0
ATOMS13the atoms involved for each of the torsions you wish to calculate=3,1,32,31 REFERENCE13the reference values for each of the torsional angles=-1.0
ATOMS14the atoms involved for each of the torsions you wish to calculate=31,29,55,54 REFERENCE14the reference values for each of the torsional angles=-1.0
ATOMS15the atoms involved for each of the torsions you wish to calculate=54,52,78,77 REFERENCE15the reference values for each of the torsional angles=-1.0
ATOMS16the atoms involved for each of the torsions you wish to calculate=77,75,101,100 REFERENCE16the reference values for each of the torsional angles=-1.0
ATOMS17the atoms involved for each of the torsions you wish to calculate=100,98,124,123 REFERENCE17the reference values for each of the torsional angles=-1.0
ATOMS18the atoms involved for each of the torsions you wish to calculate=123,121,147,146 REFERENCE18the reference values for each of the torsional angles=-1.0
ATOMS19the atoms involved for each of the torsions you wish to calculate=146,144,170,169 REFERENCE19the reference values for each of the torsional angles=-1.0
ATOMS20the atoms involved for each of the torsions you wish to calculate=169,167,193,192 REFERENCE20the reference values for each of the torsional angles=-1.0
ATOMS21the atoms involved for each of the torsions you wish to calculate=192,190,216,215 REFERENCE21the reference values for each of the torsional angles=-1.0
ATOMS22the atoms involved for each of the torsions you wish to calculate=215,213,239,238 REFERENCE22the reference values for each of the torsional angles=-1.0
ATOMS23the atoms involved for each of the torsions you wish to calculate=238,236,261,259 REFERENCE23the reference values for each of the torsional angles=-1.0
ATOMS24the atoms involved for each of the torsions you wish to calculate=4,3,1,32 REFERENCE24the reference values for each of the torsional angles=3.14
ATOMS25the atoms involved for each of the torsions you wish to calculate=32,31,29,55 REFERENCE25the reference values for each of the torsional angles=3.14
ATOMS26the atoms involved for each of the torsions you wish to calculate=55,54,52,78 REFERENCE26the reference values for each of the torsional angles=3.14
ATOMS27the atoms involved for each of the torsions you wish to calculate=78,77,75,101 REFERENCE27the reference values for each of the torsional angles=3.14
ATOMS28the atoms involved for each of the torsions you wish to calculate=101,100,98,124 REFERENCE28the reference values for each of the torsional angles=3.14
ATOMS29the atoms involved for each of the torsions you wish to calculate=124,123,121,147 REFERENCE29the reference values for each of the torsional angles=3.14
ATOMS30the atoms involved for each of the torsions you wish to calculate=147,146,144,170 REFERENCE30the reference values for each of the torsional angles=3.14
ATOMS31the atoms involved for each of the torsions you wish to calculate=170,169,167,193 REFERENCE31the reference values for each of the torsional angles=3.14
ATOMS32the atoms involved for each of the torsions you wish to calculate=193,192,190,216 REFERENCE32the reference values for each of the torsional angles=3.14
ATOMS33the atoms involved for each of the torsions you wish to calculate=216,215,213,239 REFERENCE33the reference values for each of the torsional angles=3.14
ATOMS34the atoms involved for each of the torsions you wish to calculate=239,238,236,261 REFERENCE34the reference values for each of the torsional angles=3.14
LABELa label for the action so that its output can be referenced in the input to other actions=alpha_minus_trans
... ALPHABETA

#c7beta+ cis
The ALPHABETA action with label alpha_minus_trans calculates the following quantities:
 Quantity   
 Description  
alpha_minus_trans.value
the alpha beta CVALPHABETAMeasures a distance including pbc between the instantaneous values of a set of torsional angles and set of reference values. More details ...
ATOMS1the atoms involved for each of the torsions you wish to calculate=24,4,3,1 REFERENCE1the reference values for each of the torsional angles=2.09
ATOMS2the atoms involved for each of the torsions you wish to calculate=1,32,31,29 REFERENCE2the reference values for each of the torsional angles=2.09
ATOMS3the atoms involved for each of the torsions you wish to calculate=29,55,54,52 REFERENCE3the reference values for each of the torsional angles=2.09
ATOMS4the atoms involved for each of the torsions you wish to calculate=52,78,77,75 REFERENCE4the reference values for each of the torsional angles=2.09
ATOMS5the atoms involved for each of the torsions you wish to calculate=75,101,100,98 REFERENCE5the reference values for each of the torsional angles=2.09
ATOMS6the atoms involved for each of the torsions you wish to calculate=98,124,123,121 REFERENCE6the reference values for each of the torsional angles=2.09
ATOMS7the atoms involved for each of the torsions you wish to calculate=121,147,146,144 REFERENCE7the reference values for each of the torsional angles=2.09
ATOMS8the atoms involved for each of the torsions you wish to calculate=144,170,169,167 REFERENCE8the reference values for each of the torsional angles=2.09
ATOMS9the atoms involved for each of the torsions you wish to calculate=167,193,192,190 REFERENCE9the reference values for each of the torsional angles=2.09
ATOMS10the atoms involved for each of the torsions you wish to calculate=190,216,215,213 REFERENCE10the reference values for each of the torsional angles=2.09
ATOMS11the atoms involved for each of the torsions you wish to calculate=213,239,238,236 REFERENCE11the reference values for each of the torsional angles=2.09
ATOMS12the atoms involved for each of the torsions you wish to calculate=26,24,4,3 REFERENCE12the reference values for each of the torsional angles=-1.3
ATOMS13the atoms involved for each of the torsions you wish to calculate=3,1,32,31 REFERENCE13the reference values for each of the torsional angles=-1.3
ATOMS14the atoms involved for each of the torsions you wish to calculate=31,29,55,54 REFERENCE14the reference values for each of the torsional angles=-1.3
ATOMS15the atoms involved for each of the torsions you wish to calculate=54,52,78,77 REFERENCE15the reference values for each of the torsional angles=-1.3
ATOMS16the atoms involved for each of the torsions you wish to calculate=77,75,101,100 REFERENCE16the reference values for each of the torsional angles=-1.3
ATOMS17the atoms involved for each of the torsions you wish to calculate=100,98,124,123 REFERENCE17the reference values for each of the torsional angles=-1.3
ATOMS18the atoms involved for each of the torsions you wish to calculate=123,121,147,146 REFERENCE18the reference values for each of the torsional angles=-1.3
ATOMS19the atoms involved for each of the torsions you wish to calculate=146,144,170,169 REFERENCE19the reference values for each of the torsional angles=-1.3
ATOMS20the atoms involved for each of the torsions you wish to calculate=169,167,193,192 REFERENCE20the reference values for each of the torsional angles=-1.3
ATOMS21the atoms involved for each of the torsions you wish to calculate=192,190,216,215 REFERENCE21the reference values for each of the torsional angles=-1.3
ATOMS22the atoms involved for each of the torsions you wish to calculate=215,213,239,238 REFERENCE22the reference values for each of the torsional angles=-1.3
ATOMS23the atoms involved for each of the torsions you wish to calculate=238,236,261,259 REFERENCE23the reference values for each of the torsional angles=-1.3
ATOMS24the atoms involved for each of the torsions you wish to calculate=4,3,1,32 REFERENCE24the reference values for each of the torsional angles=0
ATOMS25the atoms involved for each of the torsions you wish to calculate=32,31,29,55 REFERENCE25the reference values for each of the torsional angles=0
ATOMS26the atoms involved for each of the torsions you wish to calculate=55,54,52,78 REFERENCE26the reference values for each of the torsional angles=0
ATOMS27the atoms involved for each of the torsions you wish to calculate=78,77,75,101 REFERENCE27the reference values for each of the torsional angles=0
ATOMS28the atoms involved for each of the torsions you wish to calculate=101,100,98,124 REFERENCE28the reference values for each of the torsional angles=0
ATOMS29the atoms involved for each of the torsions you wish to calculate=124,123,121,147 REFERENCE29the reference values for each of the torsional angles=0
ATOMS30the atoms involved for each of the torsions you wish to calculate=147,146,144,170 REFERENCE30the reference values for each of the torsional angles=0
ATOMS31the atoms involved for each of the torsions you wish to calculate=170,169,167,193 REFERENCE31the reference values for each of the torsional angles=0
ATOMS32the atoms involved for each of the torsions you wish to calculate=193,192,190,216 REFERENCE32the reference values for each of the torsional angles=0
ATOMS33the atoms involved for each of the torsions you wish to calculate=216,215,213,239 REFERENCE33the reference values for each of the torsional angles=0
ATOMS34the atoms involved for each of the torsions you wish to calculate=239,238,236,261 REFERENCE34the reference values for each of the torsional angles=0
LABELa label for the action so that its output can be referenced in the input to other actions=c7beta_plus
... ALPHABETA

#c7beta+ trans
The ALPHABETA action with label c7beta_plus calculates the following quantities:
 Quantity   
 Description  
c7beta_plus.value
the alpha beta CVALPHABETAMeasures a distance including pbc between the instantaneous values of a set of torsional angles and set of reference values. More details ...
ATOMS1the atoms involved for each of the torsions you wish to calculate=24,4,3,1 REFERENCE1the reference values for each of the torsional angles=2.09
ATOMS2the atoms involved for each of the torsions you wish to calculate=1,32,31,29 REFERENCE2the reference values for each of the torsional angles=2.09
ATOMS3the atoms involved for each of the torsions you wish to calculate=29,55,54,52 REFERENCE3the reference values for each of the torsional angles=2.09
ATOMS4the atoms involved for each of the torsions you wish to calculate=52,78,77,75 REFERENCE4the reference values for each of the torsional angles=2.09
ATOMS5the atoms involved for each of the torsions you wish to calculate=75,101,100,98 REFERENCE5the reference values for each of the torsional angles=2.09
ATOMS6the atoms involved for each of the torsions you wish to calculate=98,124,123,121 REFERENCE6the reference values for each of the torsional angles=2.09
ATOMS7the atoms involved for each of the torsions you wish to calculate=121,147,146,144 REFERENCE7the reference values for each of the torsional angles=2.09
ATOMS8the atoms involved for each of the torsions you wish to calculate=144,170,169,167 REFERENCE8the reference values for each of the torsional angles=2.09
ATOMS9the atoms involved for each of the torsions you wish to calculate=167,193,192,190 REFERENCE9the reference values for each of the torsional angles=2.09
ATOMS10the atoms involved for each of the torsions you wish to calculate=190,216,215,213 REFERENCE10the reference values for each of the torsional angles=2.09
ATOMS11the atoms involved for each of the torsions you wish to calculate=213,239,238,236 REFERENCE11the reference values for each of the torsional angles=2.09
ATOMS12the atoms involved for each of the torsions you wish to calculate=26,24,4,3 REFERENCE12the reference values for each of the torsional angles=-1.3
ATOMS13the atoms involved for each of the torsions you wish to calculate=3,1,32,31 REFERENCE13the reference values for each of the torsional angles=-1.3
ATOMS14the atoms involved for each of the torsions you wish to calculate=31,29,55,54 REFERENCE14the reference values for each of the torsional angles=-1.3
ATOMS15the atoms involved for each of the torsions you wish to calculate=54,52,78,77 REFERENCE15the reference values for each of the torsional angles=-1.3
ATOMS16the atoms involved for each of the torsions you wish to calculate=77,75,101,100 REFERENCE16the reference values for each of the torsional angles=-1.3
ATOMS17the atoms involved for each of the torsions you wish to calculate=100,98,124,123 REFERENCE17the reference values for each of the torsional angles=-1.3
ATOMS18the atoms involved for each of the torsions you wish to calculate=123,121,147,146 REFERENCE18the reference values for each of the torsional angles=-1.3
ATOMS19the atoms involved for each of the torsions you wish to calculate=146,144,170,169 REFERENCE19the reference values for each of the torsional angles=-1.3
ATOMS20the atoms involved for each of the torsions you wish to calculate=169,167,193,192 REFERENCE20the reference values for each of the torsional angles=-1.3
ATOMS21the atoms involved for each of the torsions you wish to calculate=192,190,216,215 REFERENCE21the reference values for each of the torsional angles=-1.3
ATOMS22the atoms involved for each of the torsions you wish to calculate=215,213,239,238 REFERENCE22the reference values for each of the torsional angles=-1.3
ATOMS23the atoms involved for each of the torsions you wish to calculate=238,236,261,259 REFERENCE23the reference values for each of the torsional angles=-1.3
ATOMS24the atoms involved for each of the torsions you wish to calculate=4,3,1,32 REFERENCE24the reference values for each of the torsional angles=3.14
ATOMS25the atoms involved for each of the torsions you wish to calculate=32,31,29,55 REFERENCE25the reference values for each of the torsional angles=3.14
ATOMS26the atoms involved for each of the torsions you wish to calculate=55,54,52,78 REFERENCE26the reference values for each of the torsional angles=3.14
ATOMS27the atoms involved for each of the torsions you wish to calculate=78,77,75,101 REFERENCE27the reference values for each of the torsional angles=3.14
ATOMS28the atoms involved for each of the torsions you wish to calculate=101,100,98,124 REFERENCE28the reference values for each of the torsional angles=3.14
ATOMS29the atoms involved for each of the torsions you wish to calculate=124,123,121,147 REFERENCE29the reference values for each of the torsional angles=3.14
ATOMS30the atoms involved for each of the torsions you wish to calculate=147,146,144,170 REFERENCE30the reference values for each of the torsional angles=3.14
ATOMS31the atoms involved for each of the torsions you wish to calculate=170,169,167,193 REFERENCE31the reference values for each of the torsional angles=3.14
ATOMS32the atoms involved for each of the torsions you wish to calculate=193,192,190,216 REFERENCE32the reference values for each of the torsional angles=3.14
ATOMS33the atoms involved for each of the torsions you wish to calculate=216,215,213,239 REFERENCE33the reference values for each of the torsional angles=3.14
ATOMS34the atoms involved for each of the torsions you wish to calculate=239,238,236,261 REFERENCE34the reference values for each of the torsional angles=3.14
LABELa label for the action so that its output can be referenced in the input to other actions=c7beta_plus_trans
... ALPHABETA

#c7beta- cis
The ALPHABETA action with label c7beta_plus_trans calculates the following quantities:
 Quantity   
 Description  
c7beta_plus_trans.value
the alpha beta CVALPHABETAMeasures a distance including pbc between the instantaneous values of a set of torsional angles and set of reference values. More details ...
ATOMS1the atoms involved for each of the torsions you wish to calculate=24,4,3,1 REFERENCE1the reference values for each of the torsional angles=-2.09
ATOMS2the atoms involved for each of the torsions you wish to calculate=1,32,31,29 REFERENCE2the reference values for each of the torsional angles=-2.09
ATOMS3the atoms involved for each of the torsions you wish to calculate=29,55,54,52 REFERENCE3the reference values for each of the torsional angles=-2.09
ATOMS4the atoms involved for each of the torsions you wish to calculate=52,78,77,75 REFERENCE4the reference values for each of the torsional angles=-2.09
ATOMS5the atoms involved for each of the torsions you wish to calculate=75,101,100,98 REFERENCE5the reference values for each of the torsional angles=-2.09
ATOMS6the atoms involved for each of the torsions you wish to calculate=98,124,123,121 REFERENCE6the reference values for each of the torsional angles=-2.09
ATOMS7the atoms involved for each of the torsions you wish to calculate=121,147,146,144 REFERENCE7the reference values for each of the torsional angles=-2.09
ATOMS8the atoms involved for each of the torsions you wish to calculate=144,170,169,167 REFERENCE8the reference values for each of the torsional angles=-2.09
ATOMS9the atoms involved for each of the torsions you wish to calculate=167,193,192,190 REFERENCE9the reference values for each of the torsional angles=-2.09
ATOMS10the atoms involved for each of the torsions you wish to calculate=190,216,215,213 REFERENCE10the reference values for each of the torsional angles=-2.09
ATOMS11the atoms involved for each of the torsions you wish to calculate=213,239,238,236 REFERENCE11the reference values for each of the torsional angles=-2.09
ATOMS12the atoms involved for each of the torsions you wish to calculate=26,24,4,3 REFERENCE12the reference values for each of the torsional angles=1.3
ATOMS13the atoms involved for each of the torsions you wish to calculate=3,1,32,31 REFERENCE13the reference values for each of the torsional angles=1.3
ATOMS14the atoms involved for each of the torsions you wish to calculate=31,29,55,54 REFERENCE14the reference values for each of the torsional angles=1.3
ATOMS15the atoms involved for each of the torsions you wish to calculate=54,52,78,77 REFERENCE15the reference values for each of the torsional angles=1.3
ATOMS16the atoms involved for each of the torsions you wish to calculate=77,75,101,100 REFERENCE16the reference values for each of the torsional angles=1.3
ATOMS17the atoms involved for each of the torsions you wish to calculate=100,98,124,123 REFERENCE17the reference values for each of the torsional angles=1.3
ATOMS18the atoms involved for each of the torsions you wish to calculate=123,121,147,146 REFERENCE18the reference values for each of the torsional angles=1.3
ATOMS19the atoms involved for each of the torsions you wish to calculate=146,144,170,169 REFERENCE19the reference values for each of the torsional angles=1.3
ATOMS20the atoms involved for each of the torsions you wish to calculate=169,167,193,192 REFERENCE20the reference values for each of the torsional angles=1.3
ATOMS21the atoms involved for each of the torsions you wish to calculate=192,190,216,215 REFERENCE21the reference values for each of the torsional angles=1.3
ATOMS22the atoms involved for each of the torsions you wish to calculate=215,213,239,238 REFERENCE22the reference values for each of the torsional angles=1.3
ATOMS23the atoms involved for each of the torsions you wish to calculate=238,236,261,259 REFERENCE23the reference values for each of the torsional angles=1.3
ATOMS24the atoms involved for each of the torsions you wish to calculate=4,3,1,32 REFERENCE24the reference values for each of the torsional angles=0
ATOMS25the atoms involved for each of the torsions you wish to calculate=32,31,29,55 REFERENCE25the reference values for each of the torsional angles=0
ATOMS26the atoms involved for each of the torsions you wish to calculate=55,54,52,78 REFERENCE26the reference values for each of the torsional angles=0
ATOMS27the atoms involved for each of the torsions you wish to calculate=78,77,75,101 REFERENCE27the reference values for each of the torsional angles=0
ATOMS28the atoms involved for each of the torsions you wish to calculate=101,100,98,124 REFERENCE28the reference values for each of the torsional angles=0
ATOMS29the atoms involved for each of the torsions you wish to calculate=124,123,121,147 REFERENCE29the reference values for each of the torsional angles=0
ATOMS30the atoms involved for each of the torsions you wish to calculate=147,146,144,170 REFERENCE30the reference values for each of the torsional angles=0
ATOMS31the atoms involved for each of the torsions you wish to calculate=170,169,167,193 REFERENCE31the reference values for each of the torsional angles=0
ATOMS32the atoms involved for each of the torsions you wish to calculate=193,192,190,216 REFERENCE32the reference values for each of the torsional angles=0
ATOMS33the atoms involved for each of the torsions you wish to calculate=216,215,213,239 REFERENCE33the reference values for each of the torsional angles=0
ATOMS34the atoms involved for each of the torsions you wish to calculate=239,238,236,261 REFERENCE34the reference values for each of the torsional angles=0
LABELa label for the action so that its output can be referenced in the input to other actions=c7beta_minus
... ALPHABETA

#c7beta+ trans
The ALPHABETA action with label c7beta_minus calculates the following quantities:
 Quantity   
 Description  
c7beta_minus.value
the alpha beta CVALPHABETAMeasures a distance including pbc between the instantaneous values of a set of torsional angles and set of reference values. More details ...
ATOMS1the atoms involved for each of the torsions you wish to calculate=24,4,3,1 REFERENCE1the reference values for each of the torsional angles=-2.09
ATOMS2the atoms involved for each of the torsions you wish to calculate=1,32,31,29 REFERENCE2the reference values for each of the torsional angles=-2.09
ATOMS3the atoms involved for each of the torsions you wish to calculate=29,55,54,52 REFERENCE3the reference values for each of the torsional angles=-2.09
ATOMS4the atoms involved for each of the torsions you wish to calculate=52,78,77,75 REFERENCE4the reference values for each of the torsional angles=-2.09
ATOMS5the atoms involved for each of the torsions you wish to calculate=75,101,100,98 REFERENCE5the reference values for each of the torsional angles=-2.09
ATOMS6the atoms involved for each of the torsions you wish to calculate=98,124,123,121 REFERENCE6the reference values for each of the torsional angles=-2.09
ATOMS7the atoms involved for each of the torsions you wish to calculate=121,147,146,144 REFERENCE7the reference values for each of the torsional angles=-2.09
ATOMS8the atoms involved for each of the torsions you wish to calculate=144,170,169,167 REFERENCE8the reference values for each of the torsional angles=-2.09
ATOMS9the atoms involved for each of the torsions you wish to calculate=167,193,192,190 REFERENCE9the reference values for each of the torsional angles=-2.09
ATOMS10the atoms involved for each of the torsions you wish to calculate=190,216,215,213 REFERENCE10the reference values for each of the torsional angles=-2.09
ATOMS11the atoms involved for each of the torsions you wish to calculate=213,239,238,236 REFERENCE11the reference values for each of the torsional angles=-2.09
ATOMS12the atoms involved for each of the torsions you wish to calculate=26,24,4,3 REFERENCE12the reference values for each of the torsional angles=1.3
ATOMS13the atoms involved for each of the torsions you wish to calculate=3,1,32,31 REFERENCE13the reference values for each of the torsional angles=1.3
ATOMS14the atoms involved for each of the torsions you wish to calculate=31,29,55,54 REFERENCE14the reference values for each of the torsional angles=1.3
ATOMS15the atoms involved for each of the torsions you wish to calculate=54,52,78,77 REFERENCE15the reference values for each of the torsional angles=1.3
ATOMS16the atoms involved for each of the torsions you wish to calculate=77,75,101,100 REFERENCE16the reference values for each of the torsional angles=1.3
ATOMS17the atoms involved for each of the torsions you wish to calculate=100,98,124,123 REFERENCE17the reference values for each of the torsional angles=1.3
ATOMS18the atoms involved for each of the torsions you wish to calculate=123,121,147,146 REFERENCE18the reference values for each of the torsional angles=1.3
ATOMS19the atoms involved for each of the torsions you wish to calculate=146,144,170,169 REFERENCE19the reference values for each of the torsional angles=1.3
ATOMS20the atoms involved for each of the torsions you wish to calculate=169,167,193,192 REFERENCE20the reference values for each of the torsional angles=1.3
ATOMS21the atoms involved for each of the torsions you wish to calculate=192,190,216,215 REFERENCE21the reference values for each of the torsional angles=1.3
ATOMS22the atoms involved for each of the torsions you wish to calculate=215,213,239,238 REFERENCE22the reference values for each of the torsional angles=1.3
ATOMS23the atoms involved for each of the torsions you wish to calculate=238,236,261,259 REFERENCE23the reference values for each of the torsional angles=1.3
ATOMS24the atoms involved for each of the torsions you wish to calculate=4,3,1,32 REFERENCE24the reference values for each of the torsional angles=3.14
ATOMS25the atoms involved for each of the torsions you wish to calculate=32,31,29,55 REFERENCE25the reference values for each of the torsional angles=3.14
ATOMS26the atoms involved for each of the torsions you wish to calculate=55,54,52,78 REFERENCE26the reference values for each of the torsional angles=3.14
ATOMS27the atoms involved for each of the torsions you wish to calculate=78,77,75,101 REFERENCE27the reference values for each of the torsional angles=3.14
ATOMS28the atoms involved for each of the torsions you wish to calculate=101,100,98,124 REFERENCE28the reference values for each of the torsional angles=3.14
ATOMS29the atoms involved for each of the torsions you wish to calculate=124,123,121,147 REFERENCE29the reference values for each of the torsional angles=3.14
ATOMS30the atoms involved for each of the torsions you wish to calculate=147,146,144,170 REFERENCE30the reference values for each of the torsional angles=3.14
ATOMS31the atoms involved for each of the torsions you wish to calculate=170,169,167,193 REFERENCE31the reference values for each of the torsional angles=3.14
ATOMS32the atoms involved for each of the torsions you wish to calculate=193,192,190,216 REFERENCE32the reference values for each of the torsional angles=3.14
ATOMS33the atoms involved for each of the torsions you wish to calculate=216,215,213,239 REFERENCE33the reference values for each of the torsional angles=3.14
ATOMS34the atoms involved for each of the torsions you wish to calculate=239,238,236,261 REFERENCE34the reference values for each of the torsional angles=3.14
LABELa label for the action so that its output can be referenced in the input to other actions=c7beta_minus_trans
... ALPHABETA
# --- End of included input --- 
# WTE
The ALPHABETA action with label c7beta_minus_trans calculates the following quantities:
 Quantity   
 Description  
c7beta_minus_trans.value
the alpha beta CVMETADUsed to performed metadynamics on one or more collective variables. More details ...
ARGthe labels of the scalars on which the bias will act=ene
PACEthe frequency for hill addition=5000 BIASFACTORuse well tempered metadynamics and use this bias factor=60.0 HEIGHTthe heights of the Gaussian hills=2.0
SIGMAthe widths of the Gaussian hills=150
GRID_MINthe lower bounds for the grid=-500000 GRID_MAXthe upper bounds for the grid=-100000
FILE a file in which the list of added hills is stored=../HILLS_ene
LABELa label for the action so that its output can be referenced in the input to other actions=wtemetad
... METAD

The METAD action with label wtemetad calculates the following quantities:
 Quantity   
 Description  
wtemetad.bias
the instantaneous value of the bias potentialPBMETADUsed to performed Parallel Bias metadynamics. More details ...
  ARGthe labels of the scalars on which the bias will act=c,c1,c2,c3,c4,c5,c6,c7,c8,c9,c10,c11,c12,c13,c14,c15,c16,c17,c18,c19,c20,c21,c22,c23,c24,c25,c26,c27,c28,c29,c30,c31,c32,c33,c34,c35,c36,c37,c38,c39,c40,c41,c42,c43,c44,c45,c46,c47,c48,c49,c50,c51,c52,c53,c54,c55,c56,c57,c58,c59,c60,c61,c62,c63,c64,c65,c66,rg,alpha_d_plus,alpha_d_minus,alpha_plus,alpha_minus,c7beta_plus,c7beta_minus,alpha_d_plus_trans,alpha_d_minus_trans,alpha_plus_trans,alpha_minus_trans,c7beta_plus_trans,c7beta_minus_trans,omega0,omega1,omega2,omega3,omega4,omega5,omega6,omega7,omega8,omega9,omega10,phi0,phi1,phi2,phi3,phi4,phi5,phi6,phi7,phi8,phi9,phi10,psi0,psi1,psi2,psi3,psi4,psi5,psi6,psi7,psi8,psi9,psi10,psi11,chi0,chi1,chi2,chi3,chi4,chi5,chi6,chi7,chi8,chi9,chi10,chi11,chi20,chi21,chi22,chi23,chi24,chi25,chi26,chi27,chi28,chi29,chi210,chi211
  SIGMAthe widths of the Gaussian hills=0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.1,1,1,1,1,1,1,1,1,1,1,1,1,0.35,0.35,0.35,0.35,0.35,0.35,0.35,0.35,0.35,0.35,0.35,0.35,0.35,0.35,0.35,0.35,0.35,0.35,0.35,0.35,0.35,0.35,0.35,0.35,0.35,0.35,0.35,0.35,0.35,0.35,0.35,0.35,0.35,0.35,0.35,0.35,0.35,0.35,0.35,0.35,0.35,0.35,0.35,0.35,0.35,0.35,0.35,0.35,0.35,0.35,0.35,0.35,0.35,0.35,0.35,0.35,0.35,0.35
  HEIGHTthe height of the Gaussian hills, one for all biases=2.5 #kj/mol
  PACEthe frequency for hill addition, one for all biases=1000
  BIASFACTORuse well tempered metadynamics with this bias factor, one for all biases=140 #max rule baseBF x sqrt(NCV) ~ 100 (BF = ~12 for 10kcal/mol hill height cis/trans isom, CV=131)
#  TEMP=300
  GRID_MINthe lower bounds for the grid=-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,0,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi
  GRID_MAXthe upper bounds for the grid=40,20,20,20,20,20,20,20,20,20,20,20,20,20,20,20,20,20,20,20,20,20,20,20,20,20,20,20,20,20,20,20,20,20,20,20,20,20,20,20,20,20,20,20,20,20,20,20,20,20,20,20,20,20,20,20,20,20,20,20,20,20,20,20,20,20,20,3,50,50,50,50,50,50,50,50,50,50,50,50,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi
  LABELa label for the action so that its output can be referenced in the input to other actions=pb
  FILEfiles in which the lists of added hills are stored, default names are assigned using arguments if FILE is not found=../HILLS_cn,../HILLS_c1,../HILLS_c2,../HILLS_c3,../HILLS_c4,../HILLS_c5,../HILLS_c6,../HILLS_c7,../HILLS_c8,../HILLS_c9,../HILLS_c10,../HILLS_c11,../HILLS_c12,../HILLS_c13,../HILLS_c14,../HILLS_c15,../HILLS_c16,../HILLS_c17,../HILLS_c18,../HILLS_c19,../HILLS_c20,../HILLS_c21,../HILLS_c22,../HILLS_c23,../HILLS_c24,../HILLS_c25,../HILLS_c26,../HILLS_c27,../HILLS_c28,../HILLS_c29,../HILLS_c30,../HILLS_c31,../HILLS_c32,../HILLS_c33,../HILLS_c34,../HILLS_c35,../HILLS_c36,../HILLS_c37,../HILLS_c38,../HILLS_c39,../HILLS_c40,../HILLS_c41,../HILLS_c42,../HILLS_c43,../HILLS_c44,../HILLS_c45,../HILLS_c46,../HILLS_c47,../HILLS_c48,../HILLS_c49,../HILLS_c50,../HILLS_c51,../HILLS_c52,../HILLS_c53,../HILLS_c54,../HILLS_c55,../HILLS_c56,../HILLS_c57,../HILLS_c58,../HILLS_c59,../HILLS_c60,../HILLS_c61,../HILLS_c62,../HILLS_c63,../HILLS_c64,../HILLS_c65,../HILLS_c66,../HILLS_rg,../HILLS_alpha_d_plus,../HILLS_alpha_d_minus,../HILLS_alpha_plus,../HILLS_alpha_minus,../HILLS_c7beta_plus,../HILLS_c7beta_minus,../HILLS_alpha_d_plus_trans,../HILLS_alpha_d_minus_trans,../HILLS_alpha_plus_trans,../HILLS_alpha_minus_trans,../HILLS_c7beta_plus_trans,../HILLS_c7beta_minus_trans,../HILLS_omega0,../HILLS_omega1,../HILLS_omega2,../HILLS_omega3,../HILLS_omega4,../HILLS_omega5,../HILLS_omega6,../HILLS_omega7,../HILLS_omega8,../HILLS_omega9,../HILLS_omega10,../HILLS_phi0,../HILLS_phi1,../HILLS_phi2,../HILLS_phi3,../HILLS_phi4,../HILLS_phi5,../HILLS_phi6,../HILLS_phi7,../HILLS_phi8,../HILLS_phi9,../HILLS_phi10,../HILLS_psi0,../HILLS_psi1,../HILLS_psi2,../HILLS_psi3,../HILLS_psi4,../HILLS_psi5,../HILLS_psi6,../HILLS_psi7,../HILLS_psi8,../HILLS_psi9,../HILLS_psi10,../HILLS_psi11,../HILLS_chi0,../HILLS_chi1,../HILLS_chi2,../HILLS_chi3,../HILLS_chi4,../HILLS_chi5,../HILLS_chi6,../HILLS_chi7,../HILLS_chi8,../HILLS_chi9,../HILLS_chi10,../HILLS_chi11,../HILLS_chi20,../HILLS_chi21,../HILLS_chi22,../HILLS_chi23,../HILLS_chi24,../HILLS_chi25,../HILLS_chi26,../HILLS_chi27,../HILLS_chi28,../HILLS_chi29,../HILLS_chi210,../HILLS_chi211
... PBMETAD

The PBMETAD action with label pb calculates the following quantities:
 Quantity   
 Description  
pb.bias
the instantaneous value of the bias potentialPRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=* STRIDE the frequency with which the quantities of interest should be output=1000 FILEthe name of the file on which to output these quantities=COLVAR