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
#! 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 fileFILE=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=plumedfile to be included
# coordination The INCLUDE action with label cn.dat calculates somethingr1:COMCalculate the center of mass for a group of atoms. More detailsATOMS=13,22 #res 1 and 10 agg in trial 1 The COM action with label r1 calculates somethingr2:the list of atoms which are involved the virtual atom's definitionCOMCalculate the center of mass for a group of atoms. More detailsATOMS=41,50 The COM action with label r2 calculates somethingr3:the list of atoms which are involved the virtual atom's definitionCOMCalculate the center of mass for a group of atoms. More detailsATOMS=64,73 The COM action with label r3 calculates somethingr4:the list of atoms which are involved the virtual atom's definitionCOMCalculate the center of mass for a group of atoms. More detailsATOMS=87,96 The COM action with label r4 calculates somethingr5:the list of atoms which are involved the virtual atom's definitionCOMCalculate the center of mass for a group of atoms. More detailsATOMS=110,119 The COM action with label r5 calculates somethingr6:the list of atoms which are involved the virtual atom's definitionCOMCalculate the center of mass for a group of atoms. More detailsATOMS=133,142 #res 6 and 9 should be coordinated in a helix The COM action with label r6 calculates somethingr7:the list of atoms which are involved the virtual atom's definitionCOMCalculate the center of mass for a group of atoms. More detailsATOMS=156,165 The COM action with label r7 calculates somethingr8:the list of atoms which are involved the virtual atom's definitionCOMCalculate the center of mass for a group of atoms. More detailsATOMS=179,188 The COM action with label r8 calculates somethingr9:the list of atoms which are involved the virtual atom's definitionCOMCalculate the center of mass for a group of atoms. More detailsATOMS=202,211 #CG-CH The COM action with label r9 calculates somethingr10:the list of atoms which are involved the virtual atom's definitionCOMCalculate the center of mass for a group of atoms. More detailsATOMS=225,234 The COM action with label r10 calculates somethingr11:the list of atoms which are involved the virtual atom's definitionCOMCalculate the center of mass for a group of atoms. More detailsATOMS=248,257 The COM action with label r11 calculates somethingr12:the list of atoms which are involved the virtual atom's definitionCOMCalculate the center of mass for a group of atoms. More detailsATOMS=270,279the list of atoms which are involved the virtual atom's definition
# coordination The COM action with label r12 calculates somethingc:COORDINATIONCalculate coordination numbers. More detailsGROUPA=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,r11First list of atomsGROUPB=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,r12Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)R_0=0.5The r_0 parameter of the switching functionNN=8The n parameter of the switching functionMM=12The m parameter of the switching function; 0 implies 2*NNNLISTUse a neighbor list to speed up the calculationNL_CUTOFF=0.75The cutoff for the neighbor listNL_STRIDE=10The frequency with which we are updating the atoms in the neighbor listPAIRPair 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:c1:
Quantity Description c.value the value of the coordination COORDINATIONCalculate coordination numbers. More detailsGROUPA=r1First list of atomsGROUPB=r2Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)R_0=0.5The r_0 parameter of the switching functionNN=8The n parameter of the switching functionMM=12The m parameter of the switching function; 0 implies 2*NNNLISTUse a neighbor list to speed up the calculationNL_CUTOFF=0.75The cutoff for the neighbor listNL_STRIDE=10 The COORDINATION action with label c1 calculates the following quantities:The frequency with which we are updating the atoms in the neighbor listc2:
Quantity Description c1.value the value of the coordination COORDINATIONCalculate coordination numbers. More detailsGROUPA=r1First list of atomsGROUPB=r3Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)R_0=0.5The r_0 parameter of the switching functionNN=8The n parameter of the switching functionMM=12The m parameter of the switching function; 0 implies 2*NNNLISTUse a neighbor list to speed up the calculationNL_CUTOFF=0.75The cutoff for the neighbor listNL_STRIDE=10 The COORDINATION action with label c2 calculates the following quantities:The frequency with which we are updating the atoms in the neighbor listc3:
Quantity Description c2.value the value of the coordination COORDINATIONCalculate coordination numbers. More detailsGROUPA=r1First list of atomsGROUPB=r4Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)R_0=0.5The r_0 parameter of the switching functionNN=8The n parameter of the switching functionMM=12The m parameter of the switching function; 0 implies 2*NNNLISTUse a neighbor list to speed up the calculationNL_CUTOFF=0.75The cutoff for the neighbor listNL_STRIDE=10 The COORDINATION action with label c3 calculates the following quantities:The frequency with which we are updating the atoms in the neighbor listc4:
Quantity Description c3.value the value of the coordination COORDINATIONCalculate coordination numbers. More detailsGROUPA=r1First list of atomsGROUPB=r5Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)R_0=0.5The r_0 parameter of the switching functionNN=8The n parameter of the switching functionMM=12The m parameter of the switching function; 0 implies 2*NNNLISTUse a neighbor list to speed up the calculationNL_CUTOFF=0.75The cutoff for the neighbor listNL_STRIDE=10 The COORDINATION action with label c4 calculates the following quantities:The frequency with which we are updating the atoms in the neighbor listc5:
Quantity Description c4.value the value of the coordination COORDINATIONCalculate coordination numbers. More detailsGROUPA=r1First list of atomsGROUPB=r6Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)R_0=0.5The r_0 parameter of the switching functionNN=8The n parameter of the switching functionMM=12The m parameter of the switching function; 0 implies 2*NNNLISTUse a neighbor list to speed up the calculationNL_CUTOFF=0.75The cutoff for the neighbor listNL_STRIDE=10 The COORDINATION action with label c5 calculates the following quantities:The frequency with which we are updating the atoms in the neighbor listc6:
Quantity Description c5.value the value of the coordination COORDINATIONCalculate coordination numbers. More detailsGROUPA=r1First list of atomsGROUPB=r7Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)R_0=0.5The r_0 parameter of the switching functionNN=8The n parameter of the switching functionMM=12The m parameter of the switching function; 0 implies 2*NNNLISTUse a neighbor list to speed up the calculationNL_CUTOFF=0.75The cutoff for the neighbor listNL_STRIDE=10 The COORDINATION action with label c6 calculates the following quantities:The frequency with which we are updating the atoms in the neighbor listc7:
Quantity Description c6.value the value of the coordination COORDINATIONCalculate coordination numbers. More detailsGROUPA=r1First list of atomsGROUPB=r8Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)R_0=0.5The r_0 parameter of the switching functionNN=8The n parameter of the switching functionMM=12The m parameter of the switching function; 0 implies 2*NNNLISTUse a neighbor list to speed up the calculationNL_CUTOFF=0.75The cutoff for the neighbor listNL_STRIDE=10 The COORDINATION action with label c7 calculates the following quantities:The frequency with which we are updating the atoms in the neighbor listc8:
Quantity Description c7.value the value of the coordination COORDINATIONCalculate coordination numbers. More detailsGROUPA=r1First list of atomsGROUPB=r9Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)R_0=0.5The r_0 parameter of the switching functionNN=8The n parameter of the switching functionMM=12The m parameter of the switching function; 0 implies 2*NNNLISTUse a neighbor list to speed up the calculationNL_CUTOFF=0.75The cutoff for the neighbor listNL_STRIDE=10 The COORDINATION action with label c8 calculates the following quantities:The frequency with which we are updating the atoms in the neighbor listc9:
Quantity Description c8.value the value of the coordination COORDINATIONCalculate coordination numbers. More detailsGROUPA=r1First list of atomsGROUPB=r10Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)R_0=0.5The r_0 parameter of the switching functionNN=8The n parameter of the switching functionMM=12The m parameter of the switching function; 0 implies 2*NNNLISTUse a neighbor list to speed up the calculationNL_CUTOFF=0.75The cutoff for the neighbor listNL_STRIDE=10 The COORDINATION action with label c9 calculates the following quantities:The frequency with which we are updating the atoms in the neighbor listc10:
Quantity Description c9.value the value of the coordination COORDINATIONCalculate coordination numbers. More detailsGROUPA=r1First list of atomsGROUPB=r11Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)R_0=0.5The r_0 parameter of the switching functionNN=8The n parameter of the switching functionMM=12The m parameter of the switching function; 0 implies 2*NNNLISTUse a neighbor list to speed up the calculationNL_CUTOFF=0.75The cutoff for the neighbor listNL_STRIDE=10 The COORDINATION action with label c10 calculates the following quantities:The frequency with which we are updating the atoms in the neighbor listc11:
Quantity Description c10.value the value of the coordination COORDINATIONCalculate coordination numbers. More detailsGROUPA=r1First list of atomsGROUPB=r12Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)R_0=0.5The r_0 parameter of the switching functionNN=8The n parameter of the switching functionMM=12The m parameter of the switching function; 0 implies 2*NNNLISTUse a neighbor list to speed up the calculationNL_CUTOFF=0.75The cutoff for the neighbor listNL_STRIDE=10 The COORDINATION action with label c11 calculates the following quantities:The frequency with which we are updating the atoms in the neighbor listc12:
Quantity Description c11.value the value of the coordination COORDINATIONCalculate coordination numbers. More detailsGROUPA=r2First list of atomsGROUPB=r3Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)R_0=0.5The r_0 parameter of the switching functionNN=8The n parameter of the switching functionMM=12The m parameter of the switching function; 0 implies 2*NNNLISTUse a neighbor list to speed up the calculationNL_CUTOFF=0.75The cutoff for the neighbor listNL_STRIDE=10 The COORDINATION action with label c12 calculates the following quantities:The frequency with which we are updating the atoms in the neighbor listc13:
Quantity Description c12.value the value of the coordination COORDINATIONCalculate coordination numbers. More detailsGROUPA=r2First list of atomsGROUPB=r4Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)R_0=0.5The r_0 parameter of the switching functionNN=8The n parameter of the switching functionMM=12The m parameter of the switching function; 0 implies 2*NNNLISTUse a neighbor list to speed up the calculationNL_CUTOFF=0.75The cutoff for the neighbor listNL_STRIDE=10 The COORDINATION action with label c13 calculates the following quantities:The frequency with which we are updating the atoms in the neighbor listc14:
Quantity Description c13.value the value of the coordination COORDINATIONCalculate coordination numbers. More detailsGROUPA=r2First list of atomsGROUPB=r5Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)R_0=0.5The r_0 parameter of the switching functionNN=8The n parameter of the switching functionMM=12The m parameter of the switching function; 0 implies 2*NNNLISTUse a neighbor list to speed up the calculationNL_CUTOFF=0.75The cutoff for the neighbor listNL_STRIDE=10 The COORDINATION action with label c14 calculates the following quantities:The frequency with which we are updating the atoms in the neighbor listc15:
Quantity Description c14.value the value of the coordination COORDINATIONCalculate coordination numbers. More detailsGROUPA=r2First list of atomsGROUPB=r6Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)R_0=0.5The r_0 parameter of the switching functionNN=8The n parameter of the switching functionMM=12The m parameter of the switching function; 0 implies 2*NNNLISTUse a neighbor list to speed up the calculationNL_CUTOFF=0.75The cutoff for the neighbor listNL_STRIDE=10 The COORDINATION action with label c15 calculates the following quantities:The frequency with which we are updating the atoms in the neighbor listc16:
Quantity Description c15.value the value of the coordination COORDINATIONCalculate coordination numbers. More detailsGROUPA=r2First list of atomsGROUPB=r7Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)R_0=0.5The r_0 parameter of the switching functionNN=8The n parameter of the switching functionMM=12The m parameter of the switching function; 0 implies 2*NNNLISTUse a neighbor list to speed up the calculationNL_CUTOFF=0.75The cutoff for the neighbor listNL_STRIDE=10 The COORDINATION action with label c16 calculates the following quantities:The frequency with which we are updating the atoms in the neighbor listc17:
Quantity Description c16.value the value of the coordination COORDINATIONCalculate coordination numbers. More detailsGROUPA=r2First list of atomsGROUPB=r8Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)R_0=0.5The r_0 parameter of the switching functionNN=8The n parameter of the switching functionMM=12The m parameter of the switching function; 0 implies 2*NNNLISTUse a neighbor list to speed up the calculationNL_CUTOFF=0.75The cutoff for the neighbor listNL_STRIDE=10 The COORDINATION action with label c17 calculates the following quantities:The frequency with which we are updating the atoms in the neighbor listc18:
Quantity Description c17.value the value of the coordination COORDINATIONCalculate coordination numbers. More detailsGROUPA=r2First list of atomsGROUPB=r9Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)R_0=0.5The r_0 parameter of the switching functionNN=8The n parameter of the switching functionMM=12The m parameter of the switching function; 0 implies 2*NNNLISTUse a neighbor list to speed up the calculationNL_CUTOFF=0.75The cutoff for the neighbor listNL_STRIDE=10 The COORDINATION action with label c18 calculates the following quantities:The frequency with which we are updating the atoms in the neighbor listc19:
Quantity Description c18.value the value of the coordination COORDINATIONCalculate coordination numbers. More detailsGROUPA=r2First list of atomsGROUPB=r10Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)R_0=0.5The r_0 parameter of the switching functionNN=8The n parameter of the switching functionMM=12The m parameter of the switching function; 0 implies 2*NNNLISTUse a neighbor list to speed up the calculationNL_CUTOFF=0.75The cutoff for the neighbor listNL_STRIDE=10 The COORDINATION action with label c19 calculates the following quantities:The frequency with which we are updating the atoms in the neighbor listc20:
Quantity Description c19.value the value of the coordination COORDINATIONCalculate coordination numbers. More detailsGROUPA=r2First list of atomsGROUPB=r11Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)R_0=0.5The r_0 parameter of the switching functionNN=8The n parameter of the switching functionMM=12The m parameter of the switching function; 0 implies 2*NNNLISTUse a neighbor list to speed up the calculationNL_CUTOFF=0.75The cutoff for the neighbor listNL_STRIDE=10 The COORDINATION action with label c20 calculates the following quantities:The frequency with which we are updating the atoms in the neighbor listc21:
Quantity Description c20.value the value of the coordination COORDINATIONCalculate coordination numbers. More detailsGROUPA=r2First list of atomsGROUPB=r12Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)R_0=0.5The r_0 parameter of the switching functionNN=8The n parameter of the switching functionMM=12The m parameter of the switching function; 0 implies 2*NNNLISTUse a neighbor list to speed up the calculationNL_CUTOFF=0.75The cutoff for the neighbor listNL_STRIDE=10 The COORDINATION action with label c21 calculates the following quantities:The frequency with which we are updating the atoms in the neighbor listc22:
Quantity Description c21.value the value of the coordination COORDINATIONCalculate coordination numbers. More detailsGROUPA=r3First list of atomsGROUPB=r4Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)R_0=0.5The r_0 parameter of the switching functionNN=8The n parameter of the switching functionMM=12The m parameter of the switching function; 0 implies 2*NNNLISTUse a neighbor list to speed up the calculationNL_CUTOFF=0.75The cutoff for the neighbor listNL_STRIDE=10 The COORDINATION action with label c22 calculates the following quantities:The frequency with which we are updating the atoms in the neighbor listc23:
Quantity Description c22.value the value of the coordination COORDINATIONCalculate coordination numbers. More detailsGROUPA=r3First list of atomsGROUPB=r5Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)R_0=0.5The r_0 parameter of the switching functionNN=8The n parameter of the switching functionMM=12The m parameter of the switching function; 0 implies 2*NNNLISTUse a neighbor list to speed up the calculationNL_CUTOFF=0.75The cutoff for the neighbor listNL_STRIDE=10 The COORDINATION action with label c23 calculates the following quantities:The frequency with which we are updating the atoms in the neighbor listc24:
Quantity Description c23.value the value of the coordination COORDINATIONCalculate coordination numbers. More detailsGROUPA=r3First list of atomsGROUPB=r6Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)R_0=0.5The r_0 parameter of the switching functionNN=8The n parameter of the switching functionMM=12The m parameter of the switching function; 0 implies 2*NNNLISTUse a neighbor list to speed up the calculationNL_CUTOFF=0.75The cutoff for the neighbor listNL_STRIDE=10 The COORDINATION action with label c24 calculates the following quantities:The frequency with which we are updating the atoms in the neighbor listc25:
Quantity Description c24.value the value of the coordination COORDINATIONCalculate coordination numbers. More detailsGROUPA=r3First list of atomsGROUPB=r7Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)R_0=0.5The r_0 parameter of the switching functionNN=8The n parameter of the switching functionMM=12The m parameter of the switching function; 0 implies 2*NNNLISTUse a neighbor list to speed up the calculationNL_CUTOFF=0.75The cutoff for the neighbor listNL_STRIDE=10 The COORDINATION action with label c25 calculates the following quantities:The frequency with which we are updating the atoms in the neighbor listc26:
Quantity Description c25.value the value of the coordination COORDINATIONCalculate coordination numbers. More detailsGROUPA=r3First list of atomsGROUPB=r8Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)R_0=0.5The r_0 parameter of the switching functionNN=8The n parameter of the switching functionMM=12The m parameter of the switching function; 0 implies 2*NNNLISTUse a neighbor list to speed up the calculationNL_CUTOFF=0.75The cutoff for the neighbor listNL_STRIDE=10 The COORDINATION action with label c26 calculates the following quantities:The frequency with which we are updating the atoms in the neighbor listc27:
Quantity Description c26.value the value of the coordination COORDINATIONCalculate coordination numbers. More detailsGROUPA=r3First list of atomsGROUPB=r9Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)R_0=0.5The r_0 parameter of the switching functionNN=8The n parameter of the switching functionMM=12The m parameter of the switching function; 0 implies 2*NNNLISTUse a neighbor list to speed up the calculationNL_CUTOFF=0.75The cutoff for the neighbor listNL_STRIDE=10 The COORDINATION action with label c27 calculates the following quantities:The frequency with which we are updating the atoms in the neighbor listc28:
Quantity Description c27.value the value of the coordination COORDINATIONCalculate coordination numbers. More detailsGROUPA=r3First list of atomsGROUPB=r10Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)R_0=0.5The r_0 parameter of the switching functionNN=8The n parameter of the switching functionMM=12The m parameter of the switching function; 0 implies 2*NNNLISTUse a neighbor list to speed up the calculationNL_CUTOFF=0.75The cutoff for the neighbor listNL_STRIDE=10 The COORDINATION action with label c28 calculates the following quantities:The frequency with which we are updating the atoms in the neighbor listc29:
Quantity Description c28.value the value of the coordination COORDINATIONCalculate coordination numbers. More detailsGROUPA=r3First list of atomsGROUPB=r11Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)R_0=0.5The r_0 parameter of the switching functionNN=8The n parameter of the switching functionMM=12The m parameter of the switching function; 0 implies 2*NNNLISTUse a neighbor list to speed up the calculationNL_CUTOFF=0.75The cutoff for the neighbor listNL_STRIDE=10 The COORDINATION action with label c29 calculates the following quantities:The frequency with which we are updating the atoms in the neighbor listc30:
Quantity Description c29.value the value of the coordination COORDINATIONCalculate coordination numbers. More detailsGROUPA=r3First list of atomsGROUPB=r12Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)R_0=0.5The r_0 parameter of the switching functionNN=8The n parameter of the switching functionMM=12The m parameter of the switching function; 0 implies 2*NNNLISTUse a neighbor list to speed up the calculationNL_CUTOFF=0.75The cutoff for the neighbor listNL_STRIDE=10 The COORDINATION action with label c30 calculates the following quantities:The frequency with which we are updating the atoms in the neighbor listc31:
Quantity Description c30.value the value of the coordination COORDINATIONCalculate coordination numbers. More detailsGROUPA=r4First list of atomsGROUPB=r5Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)R_0=0.5The r_0 parameter of the switching functionNN=8The n parameter of the switching functionMM=12The m parameter of the switching function; 0 implies 2*NNNLISTUse a neighbor list to speed up the calculationNL_CUTOFF=0.75The cutoff for the neighbor listNL_STRIDE=10 The COORDINATION action with label c31 calculates the following quantities:The frequency with which we are updating the atoms in the neighbor listc32:
Quantity Description c31.value the value of the coordination COORDINATIONCalculate coordination numbers. More detailsGROUPA=r4First list of atomsGROUPB=r6Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)R_0=0.5The r_0 parameter of the switching functionNN=8The n parameter of the switching functionMM=12The m parameter of the switching function; 0 implies 2*NNNLISTUse a neighbor list to speed up the calculationNL_CUTOFF=0.75The cutoff for the neighbor listNL_STRIDE=10 The COORDINATION action with label c32 calculates the following quantities:The frequency with which we are updating the atoms in the neighbor listc33:
Quantity Description c32.value the value of the coordination COORDINATIONCalculate coordination numbers. More detailsGROUPA=r4First list of atomsGROUPB=r7Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)R_0=0.5The r_0 parameter of the switching functionNN=8The n parameter of the switching functionMM=12The m parameter of the switching function; 0 implies 2*NNNLISTUse a neighbor list to speed up the calculationNL_CUTOFF=0.75The cutoff for the neighbor listNL_STRIDE=10 The COORDINATION action with label c33 calculates the following quantities:The frequency with which we are updating the atoms in the neighbor listc34:
Quantity Description c33.value the value of the coordination COORDINATIONCalculate coordination numbers. More detailsGROUPA=r4First list of atomsGROUPB=r8Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)R_0=0.5The r_0 parameter of the switching functionNN=8The n parameter of the switching functionMM=12The m parameter of the switching function; 0 implies 2*NNNLISTUse a neighbor list to speed up the calculationNL_CUTOFF=0.75The cutoff for the neighbor listNL_STRIDE=10 The COORDINATION action with label c34 calculates the following quantities:The frequency with which we are updating the atoms in the neighbor listc35:
Quantity Description c34.value the value of the coordination COORDINATIONCalculate coordination numbers. More detailsGROUPA=r4First list of atomsGROUPB=r9Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)R_0=0.5The r_0 parameter of the switching functionNN=8The n parameter of the switching functionMM=12The m parameter of the switching function; 0 implies 2*NNNLISTUse a neighbor list to speed up the calculationNL_CUTOFF=0.75The cutoff for the neighbor listNL_STRIDE=10 The COORDINATION action with label c35 calculates the following quantities:The frequency with which we are updating the atoms in the neighbor listc36:
Quantity Description c35.value the value of the coordination COORDINATIONCalculate coordination numbers. More detailsGROUPA=r4First list of atomsGROUPB=r10Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)R_0=0.5The r_0 parameter of the switching functionNN=8The n parameter of the switching functionMM=12The m parameter of the switching function; 0 implies 2*NNNLISTUse a neighbor list to speed up the calculationNL_CUTOFF=0.75The cutoff for the neighbor listNL_STRIDE=10 The COORDINATION action with label c36 calculates the following quantities:The frequency with which we are updating the atoms in the neighbor listc37:
Quantity Description c36.value the value of the coordination COORDINATIONCalculate coordination numbers. More detailsGROUPA=r4First list of atomsGROUPB=r11Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)R_0=0.5The r_0 parameter of the switching functionNN=8The n parameter of the switching functionMM=12The m parameter of the switching function; 0 implies 2*NNNLISTUse a neighbor list to speed up the calculationNL_CUTOFF=0.75The cutoff for the neighbor listNL_STRIDE=10 The COORDINATION action with label c37 calculates the following quantities:The frequency with which we are updating the atoms in the neighbor listc38:
Quantity Description c37.value the value of the coordination COORDINATIONCalculate coordination numbers. More detailsGROUPA=r4First list of atomsGROUPB=r12Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)R_0=0.5The r_0 parameter of the switching functionNN=8The n parameter of the switching functionMM=12The m parameter of the switching function; 0 implies 2*NNNLISTUse a neighbor list to speed up the calculationNL_CUTOFF=0.75The cutoff for the neighbor listNL_STRIDE=10 The COORDINATION action with label c38 calculates the following quantities:The frequency with which we are updating the atoms in the neighbor listc39:
Quantity Description c38.value the value of the coordination COORDINATIONCalculate coordination numbers. More detailsGROUPA=r5First list of atomsGROUPB=r6Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)R_0=0.5The r_0 parameter of the switching functionNN=8The n parameter of the switching functionMM=12The m parameter of the switching function; 0 implies 2*NNNLISTUse a neighbor list to speed up the calculationNL_CUTOFF=0.75The cutoff for the neighbor listNL_STRIDE=10 The COORDINATION action with label c39 calculates the following quantities:The frequency with which we are updating the atoms in the neighbor listc40:
Quantity Description c39.value the value of the coordination COORDINATIONCalculate coordination numbers. More detailsGROUPA=r5First list of atomsGROUPB=r7Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)R_0=0.5The r_0 parameter of the switching functionNN=8The n parameter of the switching functionMM=12The m parameter of the switching function; 0 implies 2*NNNLISTUse a neighbor list to speed up the calculationNL_CUTOFF=0.75The cutoff for the neighbor listNL_STRIDE=10 The COORDINATION action with label c40 calculates the following quantities:The frequency with which we are updating the atoms in the neighbor listc41:
Quantity Description c40.value the value of the coordination COORDINATIONCalculate coordination numbers. More detailsGROUPA=r5First list of atomsGROUPB=r8Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)R_0=0.5The r_0 parameter of the switching functionNN=8The n parameter of the switching functionMM=12The m parameter of the switching function; 0 implies 2*NNNLISTUse a neighbor list to speed up the calculationNL_CUTOFF=0.75The cutoff for the neighbor listNL_STRIDE=10 The COORDINATION action with label c41 calculates the following quantities:The frequency with which we are updating the atoms in the neighbor listc42:
Quantity Description c41.value the value of the coordination COORDINATIONCalculate coordination numbers. More detailsGROUPA=r5First list of atomsGROUPB=r9Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)R_0=0.5The r_0 parameter of the switching functionNN=8The n parameter of the switching functionMM=12The m parameter of the switching function; 0 implies 2*NNNLISTUse a neighbor list to speed up the calculationNL_CUTOFF=0.75The cutoff for the neighbor listNL_STRIDE=10 The COORDINATION action with label c42 calculates the following quantities:The frequency with which we are updating the atoms in the neighbor listc43:
Quantity Description c42.value the value of the coordination COORDINATIONCalculate coordination numbers. More detailsGROUPA=r5First list of atomsGROUPB=r10Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)R_0=0.5The r_0 parameter of the switching functionNN=8The n parameter of the switching functionMM=12The m parameter of the switching function; 0 implies 2*NNNLISTUse a neighbor list to speed up the calculationNL_CUTOFF=0.75The cutoff for the neighbor listNL_STRIDE=10 The COORDINATION action with label c43 calculates the following quantities:The frequency with which we are updating the atoms in the neighbor listc44:
Quantity Description c43.value the value of the coordination COORDINATIONCalculate coordination numbers. More detailsGROUPA=r5First list of atomsGROUPB=r11Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)R_0=0.5The r_0 parameter of the switching functionNN=8The n parameter of the switching functionMM=12The m parameter of the switching function; 0 implies 2*NNNLISTUse a neighbor list to speed up the calculationNL_CUTOFF=0.75The cutoff for the neighbor listNL_STRIDE=10 The COORDINATION action with label c44 calculates the following quantities:The frequency with which we are updating the atoms in the neighbor listc45:
Quantity Description c44.value the value of the coordination COORDINATIONCalculate coordination numbers. More detailsGROUPA=r5First list of atomsGROUPB=r12Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)R_0=0.5The r_0 parameter of the switching functionNN=8The n parameter of the switching functionMM=12The m parameter of the switching function; 0 implies 2*NNNLISTUse a neighbor list to speed up the calculationNL_CUTOFF=0.75The cutoff for the neighbor listNL_STRIDE=10 The COORDINATION action with label c45 calculates the following quantities:The frequency with which we are updating the atoms in the neighbor listc46:
Quantity Description c45.value the value of the coordination COORDINATIONCalculate coordination numbers. More detailsGROUPA=r6First list of atomsGROUPB=r7Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)R_0=0.5The r_0 parameter of the switching functionNN=8The n parameter of the switching functionMM=12The m parameter of the switching function; 0 implies 2*NNNLISTUse a neighbor list to speed up the calculationNL_CUTOFF=0.75The cutoff for the neighbor listNL_STRIDE=10 The COORDINATION action with label c46 calculates the following quantities:The frequency with which we are updating the atoms in the neighbor listc47:
Quantity Description c46.value the value of the coordination COORDINATIONCalculate coordination numbers. More detailsGROUPA=r6First list of atomsGROUPB=r8Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)R_0=0.5The r_0 parameter of the switching functionNN=8The n parameter of the switching functionMM=12The m parameter of the switching function; 0 implies 2*NNNLISTUse a neighbor list to speed up the calculationNL_CUTOFF=0.75The cutoff for the neighbor listNL_STRIDE=10 The COORDINATION action with label c47 calculates the following quantities:The frequency with which we are updating the atoms in the neighbor listc48:
Quantity Description c47.value the value of the coordination COORDINATIONCalculate coordination numbers. More detailsGROUPA=r6First list of atomsGROUPB=r9Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)R_0=0.5The r_0 parameter of the switching functionNN=8The n parameter of the switching functionMM=12The m parameter of the switching function; 0 implies 2*NNNLISTUse a neighbor list to speed up the calculationNL_CUTOFF=0.75The cutoff for the neighbor listNL_STRIDE=10 The COORDINATION action with label c48 calculates the following quantities:The frequency with which we are updating the atoms in the neighbor listc49:
Quantity Description c48.value the value of the coordination COORDINATIONCalculate coordination numbers. More detailsGROUPA=r6First list of atomsGROUPB=r10Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)R_0=0.5The r_0 parameter of the switching functionNN=8The n parameter of the switching functionMM=12The m parameter of the switching function; 0 implies 2*NNNLISTUse a neighbor list to speed up the calculationNL_CUTOFF=0.75The cutoff for the neighbor listNL_STRIDE=10 The COORDINATION action with label c49 calculates the following quantities:The frequency with which we are updating the atoms in the neighbor listc50:
Quantity Description c49.value the value of the coordination COORDINATIONCalculate coordination numbers. More detailsGROUPA=r6First list of atomsGROUPB=r11Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)R_0=0.5The r_0 parameter of the switching functionNN=8The n parameter of the switching functionMM=12The m parameter of the switching function; 0 implies 2*NNNLISTUse a neighbor list to speed up the calculationNL_CUTOFF=0.75The cutoff for the neighbor listNL_STRIDE=10 The COORDINATION action with label c50 calculates the following quantities:The frequency with which we are updating the atoms in the neighbor listc51:
Quantity Description c50.value the value of the coordination COORDINATIONCalculate coordination numbers. More detailsGROUPA=r6First list of atomsGROUPB=r12Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)R_0=0.5The r_0 parameter of the switching functionNN=8The n parameter of the switching functionMM=12The m parameter of the switching function; 0 implies 2*NNNLISTUse a neighbor list to speed up the calculationNL_CUTOFF=0.75The cutoff for the neighbor listNL_STRIDE=10 The COORDINATION action with label c51 calculates the following quantities:The frequency with which we are updating the atoms in the neighbor listc52:
Quantity Description c51.value the value of the coordination COORDINATIONCalculate coordination numbers. More detailsGROUPA=r7First list of atomsGROUPB=r8Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)R_0=0.5The r_0 parameter of the switching functionNN=8The n parameter of the switching functionMM=12The m parameter of the switching function; 0 implies 2*NNNLISTUse a neighbor list to speed up the calculationNL_CUTOFF=0.75The cutoff for the neighbor listNL_STRIDE=10 The COORDINATION action with label c52 calculates the following quantities:The frequency with which we are updating the atoms in the neighbor listc53:
Quantity Description c52.value the value of the coordination COORDINATIONCalculate coordination numbers. More detailsGROUPA=r7First list of atomsGROUPB=r9Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)R_0=0.5The r_0 parameter of the switching functionNN=8The n parameter of the switching functionMM=12The m parameter of the switching function; 0 implies 2*NNNLISTUse a neighbor list to speed up the calculationNL_CUTOFF=0.75The cutoff for the neighbor listNL_STRIDE=10 The COORDINATION action with label c53 calculates the following quantities:The frequency with which we are updating the atoms in the neighbor listc54:
Quantity Description c53.value the value of the coordination COORDINATIONCalculate coordination numbers. More detailsGROUPA=r7First list of atomsGROUPB=r10Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)R_0=0.5The r_0 parameter of the switching functionNN=8The n parameter of the switching functionMM=12The m parameter of the switching function; 0 implies 2*NNNLISTUse a neighbor list to speed up the calculationNL_CUTOFF=0.75The cutoff for the neighbor listNL_STRIDE=10 The COORDINATION action with label c54 calculates the following quantities:The frequency with which we are updating the atoms in the neighbor listc55:
Quantity Description c54.value the value of the coordination COORDINATIONCalculate coordination numbers. More detailsGROUPA=r7First list of atomsGROUPB=r11Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)R_0=0.5The r_0 parameter of the switching functionNN=8The n parameter of the switching functionMM=12The m parameter of the switching function; 0 implies 2*NNNLISTUse a neighbor list to speed up the calculationNL_CUTOFF=0.75The cutoff for the neighbor listNL_STRIDE=10 The COORDINATION action with label c55 calculates the following quantities:The frequency with which we are updating the atoms in the neighbor listc56:
Quantity Description c55.value the value of the coordination COORDINATIONCalculate coordination numbers. More detailsGROUPA=r7First list of atomsGROUPB=r12Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)R_0=0.5The r_0 parameter of the switching functionNN=8The n parameter of the switching functionMM=12The m parameter of the switching function; 0 implies 2*NNNLISTUse a neighbor list to speed up the calculationNL_CUTOFF=0.75The cutoff for the neighbor listNL_STRIDE=10 The COORDINATION action with label c56 calculates the following quantities:The frequency with which we are updating the atoms in the neighbor listc57:
Quantity Description c56.value the value of the coordination COORDINATIONCalculate coordination numbers. More detailsGROUPA=r8First list of atomsGROUPB=r9Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)R_0=0.5The r_0 parameter of the switching functionNN=8The n parameter of the switching functionMM=12The m parameter of the switching function; 0 implies 2*NNNLISTUse a neighbor list to speed up the calculationNL_CUTOFF=0.75The cutoff for the neighbor listNL_STRIDE=10 The COORDINATION action with label c57 calculates the following quantities:The frequency with which we are updating the atoms in the neighbor listc58:
Quantity Description c57.value the value of the coordination COORDINATIONCalculate coordination numbers. More detailsGROUPA=r8First list of atomsGROUPB=r10Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)R_0=0.5The r_0 parameter of the switching functionNN=8The n parameter of the switching functionMM=12The m parameter of the switching function; 0 implies 2*NNNLISTUse a neighbor list to speed up the calculationNL_CUTOFF=0.75The cutoff for the neighbor listNL_STRIDE=10 The COORDINATION action with label c58 calculates the following quantities:The frequency with which we are updating the atoms in the neighbor listc59:
Quantity Description c58.value the value of the coordination COORDINATIONCalculate coordination numbers. More detailsGROUPA=r8First list of atomsGROUPB=r11Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)R_0=0.5The r_0 parameter of the switching functionNN=8The n parameter of the switching functionMM=12The m parameter of the switching function; 0 implies 2*NNNLISTUse a neighbor list to speed up the calculationNL_CUTOFF=0.75The cutoff for the neighbor listNL_STRIDE=10 The COORDINATION action with label c59 calculates the following quantities:The frequency with which we are updating the atoms in the neighbor listc60:
Quantity Description c59.value the value of the coordination COORDINATIONCalculate coordination numbers. More detailsGROUPA=r8First list of atomsGROUPB=r12Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)R_0=0.5The r_0 parameter of the switching functionNN=8The n parameter of the switching functionMM=12The m parameter of the switching function; 0 implies 2*NNNLISTUse a neighbor list to speed up the calculationNL_CUTOFF=0.75The cutoff for the neighbor listNL_STRIDE=10 The COORDINATION action with label c60 calculates the following quantities:The frequency with which we are updating the atoms in the neighbor listc61:
Quantity Description c60.value the value of the coordination COORDINATIONCalculate coordination numbers. More detailsGROUPA=r9First list of atomsGROUPB=r10Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)R_0=0.5The r_0 parameter of the switching functionNN=8The n parameter of the switching functionMM=12The m parameter of the switching function; 0 implies 2*NNNLISTUse a neighbor list to speed up the calculationNL_CUTOFF=0.75The cutoff for the neighbor listNL_STRIDE=10 The COORDINATION action with label c61 calculates the following quantities:The frequency with which we are updating the atoms in the neighbor listc62:
Quantity Description c61.value the value of the coordination COORDINATIONCalculate coordination numbers. More detailsGROUPA=r9First list of atomsGROUPB=r11Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)R_0=0.5The r_0 parameter of the switching functionNN=8The n parameter of the switching functionMM=12The m parameter of the switching function; 0 implies 2*NNNLISTUse a neighbor list to speed up the calculationNL_CUTOFF=0.75The cutoff for the neighbor listNL_STRIDE=10 The COORDINATION action with label c62 calculates the following quantities:The frequency with which we are updating the atoms in the neighbor listc63:
Quantity Description c62.value the value of the coordination COORDINATIONCalculate coordination numbers. More detailsGROUPA=r9First list of atomsGROUPB=r12Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)R_0=0.5The r_0 parameter of the switching functionNN=8The n parameter of the switching functionMM=12The m parameter of the switching function; 0 implies 2*NNNLISTUse a neighbor list to speed up the calculationNL_CUTOFF=0.75The cutoff for the neighbor listNL_STRIDE=10 The COORDINATION action with label c63 calculates the following quantities:The frequency with which we are updating the atoms in the neighbor listc64:
Quantity Description c63.value the value of the coordination COORDINATIONCalculate coordination numbers. More detailsGROUPA=r10First list of atomsGROUPB=r11Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)R_0=0.5The r_0 parameter of the switching functionNN=8The n parameter of the switching functionMM=12The m parameter of the switching function; 0 implies 2*NNNLISTUse a neighbor list to speed up the calculationNL_CUTOFF=0.75The cutoff for the neighbor listNL_STRIDE=10 The COORDINATION action with label c64 calculates the following quantities:The frequency with which we are updating the atoms in the neighbor listc65:
Quantity Description c64.value the value of the coordination COORDINATIONCalculate coordination numbers. More detailsGROUPA=r10First list of atomsGROUPB=r12Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)R_0=0.5The r_0 parameter of the switching functionNN=8The n parameter of the switching functionMM=12The m parameter of the switching function; 0 implies 2*NNNLISTUse a neighbor list to speed up the calculationNL_CUTOFF=0.75The cutoff for the neighbor listNL_STRIDE=10 The COORDINATION action with label c65 calculates the following quantities:The frequency with which we are updating the atoms in the neighbor listc66:
Quantity Description c65.value the value of the coordination COORDINATIONCalculate coordination numbers. More detailsGROUPA=r11First list of atomsGROUPB=r12Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)R_0=0.5The r_0 parameter of the switching functionNN=8The n parameter of the switching functionMM=12The m parameter of the switching function; 0 implies 2*NNNLISTUse a neighbor list to speed up the calculationNL_CUTOFF=0.75The cutoff for the neighbor listNL_STRIDE=10The frequency with which we are updating the atoms in the neighbor list
# --- End of included input --- The COORDINATION action with label c66 calculates the following quantities:
Quantity Description c66.value the value of the coordination INCLUDEIncludes an external input file, similar to #include in C preprocessor. More details. Show included fileFILE=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=plumedfile to be included
#RESTART
# COLVARS
# rg The INCLUDE action with label cv.dat calculates somethingrg:GYRATIONCalculate the radius of gyration, or other properties related to it. More detailsTYPE=RADIUSThe type of calculation relative to the Gyration Tensor you want to performATOMS=1,3,4,29,31,32,52,54,55,75,77,78,98,100,101,121,123,124,144,146,147,167,169,170,190,192,193,213,215,216,236,238,239,259,261the group of atoms that you are calculating the Gyration Tensor for
# dihedrals # phi The GYRATION action with label rg calculates the following quantities:phi0:
Quantity Description rg.value the radius that was computed from the weights TORSIONCalculate a torsional angle. More detailsATOMS=24,4,3,1 The TORSION action with label phi0 calculates the following quantities:the four atoms involved in the torsional anglephi1:
Quantity Description phi0.value the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=1,32,31,29 The TORSION action with label phi1 calculates the following quantities:the four atoms involved in the torsional anglephi2:
Quantity Description phi1.value the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=29,55,54,52 The TORSION action with label phi2 calculates the following quantities:the four atoms involved in the torsional anglephi3:
Quantity Description phi2.value the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=52,78,77,75 The TORSION action with label phi3 calculates the following quantities:the four atoms involved in the torsional anglephi4:
Quantity Description phi3.value the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=75,101,100,98 The TORSION action with label phi4 calculates the following quantities:the four atoms involved in the torsional anglephi5:
Quantity Description phi4.value the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=98,124,123,121 The TORSION action with label phi5 calculates the following quantities:the four atoms involved in the torsional anglephi6:
Quantity Description phi5.value the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=121,147,146,144 The TORSION action with label phi6 calculates the following quantities:the four atoms involved in the torsional anglephi7:
Quantity Description phi6.value the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=144,170,169,167 The TORSION action with label phi7 calculates the following quantities:the four atoms involved in the torsional anglephi8:
Quantity Description phi7.value the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=167,193,192,190 The TORSION action with label phi8 calculates the following quantities:the four atoms involved in the torsional anglephi9:
Quantity Description phi8.value the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=190,216,215,213 The TORSION action with label phi9 calculates the following quantities:the four atoms involved in the torsional anglephi10:
Quantity Description phi9.value the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=213,239,238,236the four atoms involved in the torsional angle
# psi The TORSION action with label phi10 calculates the following quantities:psi0:
Quantity Description phi10.value the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=26,24,4,3 The TORSION action with label psi0 calculates the following quantities:the four atoms involved in the torsional anglepsi1:
Quantity Description psi0.value the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=3,1,32,31 The TORSION action with label psi1 calculates the following quantities:the four atoms involved in the torsional anglepsi2:
Quantity Description psi1.value the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=31,29,55,54 The TORSION action with label psi2 calculates the following quantities:the four atoms involved in the torsional anglepsi3:
Quantity Description psi2.value the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=54,52,78,77 The TORSION action with label psi3 calculates the following quantities:the four atoms involved in the torsional anglepsi4:
Quantity Description psi3.value the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=77,75,101,100 The TORSION action with label psi4 calculates the following quantities:the four atoms involved in the torsional anglepsi5:
Quantity Description psi4.value the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=100,98,124,123 The TORSION action with label psi5 calculates the following quantities:the four atoms involved in the torsional anglepsi6:
Quantity Description psi5.value the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=123,121,147,146 The TORSION action with label psi6 calculates the following quantities:the four atoms involved in the torsional anglepsi7:
Quantity Description psi6.value the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=146,144,170,169 The TORSION action with label psi7 calculates the following quantities:the four atoms involved in the torsional anglepsi8:
Quantity Description psi7.value the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=169,167,193,192 The TORSION action with label psi8 calculates the following quantities:the four atoms involved in the torsional anglepsi9:
Quantity Description psi8.value the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=192,190,216,215 The TORSION action with label psi9 calculates the following quantities:the four atoms involved in the torsional anglepsi10:
Quantity Description psi9.value the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=215,213,239,238 The TORSION action with label psi10 calculates the following quantities:the four atoms involved in the torsional anglepsi11:
Quantity Description psi10.value the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=238,236,261,259the four atoms involved in the torsional angle
# omega The TORSION action with label psi11 calculates the following quantities:omega0:
Quantity Description psi11.value the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=4,3,1,32 The TORSION action with label omega0 calculates the following quantities:the four atoms involved in the torsional angleomega1:
Quantity Description omega0.value the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=32,31,29,55 The TORSION action with label omega1 calculates the following quantities:the four atoms involved in the torsional angleomega2:
Quantity Description omega1.value the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=55,54,52,78 The TORSION action with label omega2 calculates the following quantities:the four atoms involved in the torsional angleomega3:
Quantity Description omega2.value the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=78,77,75,101 The TORSION action with label omega3 calculates the following quantities:the four atoms involved in the torsional angleomega4:
Quantity Description omega3.value the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=101,100,98,124 The TORSION action with label omega4 calculates the following quantities:the four atoms involved in the torsional angleomega5:
Quantity Description omega4.value the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=124,123,121,147 The TORSION action with label omega5 calculates the following quantities:the four atoms involved in the torsional angleomega6:
Quantity Description omega5.value the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=147,146,144,170 The TORSION action with label omega6 calculates the following quantities:the four atoms involved in the torsional angleomega7:
Quantity Description omega6.value the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=170,169,167,193 The TORSION action with label omega7 calculates the following quantities:the four atoms involved in the torsional angleomega8:
Quantity Description omega7.value the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=193,192,190,216 The TORSION action with label omega8 calculates the following quantities:the four atoms involved in the torsional angleomega9:
Quantity Description omega8.value the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=216,215,213,239 The TORSION action with label omega9 calculates the following quantities:the four atoms involved in the torsional angleomega10:
Quantity Description omega9.value the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=239,238,236,261the four atoms involved in the torsional angle
# chi-1 The TORSION action with label omega10 calculates the following quantities:chi0:
Quantity Description omega10.value the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=4,3,7,9 The TORSION action with label chi0 calculates the following quantities:the four atoms involved in the torsional anglechi1:
Quantity Description chi0.value the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=32,31,35,37 The TORSION action with label chi1 calculates the following quantities:the four atoms involved in the torsional anglechi2:
Quantity Description chi1.value the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=55,54,58,60 The TORSION action with label chi2 calculates the following quantities:the four atoms involved in the torsional anglechi3:
Quantity Description chi2.value the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=78,77,81,83 The TORSION action with label chi3 calculates the following quantities:the four atoms involved in the torsional anglechi4:
Quantity Description chi3.value the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=101,100,104,106 The TORSION action with label chi4 calculates the following quantities:the four atoms involved in the torsional anglechi5:
Quantity Description chi4.value the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=124,123,127,129 The TORSION action with label chi5 calculates the following quantities:the four atoms involved in the torsional anglechi6:
Quantity Description chi5.value the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=147,146,150,152 The TORSION action with label chi6 calculates the following quantities:the four atoms involved in the torsional anglechi7:
Quantity Description chi6.value the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=170,169,173,175 The TORSION action with label chi7 calculates the following quantities:the four atoms involved in the torsional anglechi8:
Quantity Description chi7.value the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=193,192,196,198 The TORSION action with label chi8 calculates the following quantities:the four atoms involved in the torsional anglechi9:
Quantity Description chi8.value the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=216,215,219,221 The TORSION action with label chi9 calculates the following quantities:the four atoms involved in the torsional anglechi10:
Quantity Description chi9.value the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=239,238,242,244 The TORSION action with label chi10 calculates the following quantities:the four atoms involved in the torsional anglechi11:
Quantity Description chi10.value the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=261,259,264,266the four atoms involved in the torsional angle
# chi-2 The TORSION action with label chi11 calculates the following quantities:chi20:
Quantity Description chi11.value the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=3,7,13,14 The TORSION action with label chi20 calculates the following quantities:the four atoms involved in the torsional anglechi21:
Quantity Description chi20.value the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=31,35,41,42 The TORSION action with label chi21 calculates the following quantities:the four atoms involved in the torsional anglechi22:
Quantity Description chi21.value the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=54,58,64,65 The TORSION action with label chi22 calculates the following quantities:the four atoms involved in the torsional anglechi23:
Quantity Description chi22.value the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=77,81,87,88 The TORSION action with label chi23 calculates the following quantities:the four atoms involved in the torsional anglechi24:
Quantity Description chi23.value the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=100,104,110,111 The TORSION action with label chi24 calculates the following quantities:the four atoms involved in the torsional anglechi25:
Quantity Description chi24.value the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=123,127,133,134 The TORSION action with label chi25 calculates the following quantities:the four atoms involved in the torsional anglechi26:
Quantity Description chi25.value the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=146,150,156,157 The TORSION action with label chi26 calculates the following quantities:the four atoms involved in the torsional anglechi27:
Quantity Description chi26.value the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=169,173,179,180 The TORSION action with label chi27 calculates the following quantities:the four atoms involved in the torsional anglechi28:
Quantity Description chi27.value the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=192,196,202,203 The TORSION action with label chi28 calculates the following quantities:the four atoms involved in the torsional anglechi29:
Quantity Description chi28.value the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=215,219,225,226 The TORSION action with label chi29 calculates the following quantities:the four atoms involved in the torsional anglechi210:
Quantity Description chi29.value the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=238,242,248,249 The TORSION action with label chi210 calculates the following quantities:the four atoms involved in the torsional anglechi211:
Quantity Description chi210.value the TORSION involving these atoms TORSIONCalculate a torsional angle. More detailsATOMS=259,264,270,271the four atoms involved in the torsional angle
# --- End of included input --- The TORSION action with label chi211 calculates the following quantities:
Quantity Description chi211.value the TORSION involving these atoms INCLUDEIncludes an external input file, similar to #include in C preprocessor. More details. Show included fileFILE=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=plumedfile to be included
#alphaD- cis The INCLUDE action with label ab.dat calculates somethingALPHABETA...Calculate the alpha beta CV More detailsATOMS1=24,4,3,1the atoms involved for each of the torsions you wish to calculateREFERENCE1=-1.57the reference values for each of the torsional anglesATOMS2=1,32,31,29the atoms involved for each of the torsions you wish to calculateREFERENCE2=-1.57the reference values for each of the torsional anglesATOMS3=29,55,54,52the atoms involved for each of the torsions you wish to calculateREFERENCE3=-1.57the reference values for each of the torsional anglesATOMS4=52,78,77,75the atoms involved for each of the torsions you wish to calculateREFERENCE4=-1.57the reference values for each of the torsional anglesATOMS5=75,101,100,98the atoms involved for each of the torsions you wish to calculateREFERENCE5=-1.57the reference values for each of the torsional anglesATOMS6=98,124,123,121the atoms involved for each of the torsions you wish to calculateREFERENCE6=-1.57the reference values for each of the torsional anglesATOMS7=121,147,146,144the atoms involved for each of the torsions you wish to calculateREFERENCE7=-1.57the reference values for each of the torsional anglesATOMS8=144,170,169,167the atoms involved for each of the torsions you wish to calculateREFERENCE8=-1.57the reference values for each of the torsional anglesATOMS9=167,193,192,190the atoms involved for each of the torsions you wish to calculateREFERENCE9=-1.57the reference values for each of the torsional anglesATOMS10=190,216,215,213the atoms involved for each of the torsions you wish to calculateREFERENCE10=-1.57the reference values for each of the torsional anglesATOMS11=213,239,238,236the atoms involved for each of the torsions you wish to calculateREFERENCE11=-1.57the reference values for each of the torsional anglesATOMS12=26,24,4,3the atoms involved for each of the torsions you wish to calculateREFERENCE12=3.14the reference values for each of the torsional anglesATOMS13=3,1,32,31the atoms involved for each of the torsions you wish to calculateREFERENCE13=3.14the reference values for each of the torsional anglesATOMS14=31,29,55,54the atoms involved for each of the torsions you wish to calculateREFERENCE14=3.14the reference values for each of the torsional anglesATOMS15=54,52,78,77the atoms involved for each of the torsions you wish to calculateREFERENCE15=3.14the reference values for each of the torsional anglesATOMS16=77,75,101,100the atoms involved for each of the torsions you wish to calculateREFERENCE16=3.14the reference values for each of the torsional anglesATOMS17=100,98,124,123the atoms involved for each of the torsions you wish to calculateREFERENCE17=3.14the reference values for each of the torsional anglesATOMS18=123,121,147,146the atoms involved for each of the torsions you wish to calculateREFERENCE18=3.14the reference values for each of the torsional anglesATOMS19=146,144,170,169the atoms involved for each of the torsions you wish to calculateREFERENCE19=3.14the reference values for each of the torsional anglesATOMS20=169,167,193,192the atoms involved for each of the torsions you wish to calculateREFERENCE20=3.14the reference values for each of the torsional anglesATOMS21=192,190,216,215the atoms involved for each of the torsions you wish to calculateREFERENCE21=3.14the reference values for each of the torsional anglesATOMS22=215,213,239,238the atoms involved for each of the torsions you wish to calculateREFERENCE22=3.14the reference values for each of the torsional anglesATOMS23=238,236,261,259the atoms involved for each of the torsions you wish to calculateREFERENCE23=3.14the reference values for each of the torsional anglesATOMS24=4,3,1,32the atoms involved for each of the torsions you wish to calculateREFERENCE24=0the reference values for each of the torsional anglesATOMS25=32,31,29,55the atoms involved for each of the torsions you wish to calculateREFERENCE25=0the reference values for each of the torsional anglesATOMS26=55,54,52,78the atoms involved for each of the torsions you wish to calculateREFERENCE26=0the reference values for each of the torsional anglesATOMS27=78,77,75,101the atoms involved for each of the torsions you wish to calculateREFERENCE27=0the reference values for each of the torsional anglesATOMS28=101,100,98,124the atoms involved for each of the torsions you wish to calculateREFERENCE28=0the reference values for each of the torsional anglesATOMS29=124,123,121,147the atoms involved for each of the torsions you wish to calculateREFERENCE29=0the reference values for each of the torsional anglesATOMS30=147,146,144,170the atoms involved for each of the torsions you wish to calculateREFERENCE30=0the reference values for each of the torsional anglesATOMS31=170,169,167,193the atoms involved for each of the torsions you wish to calculateREFERENCE31=0the reference values for each of the torsional anglesATOMS32=193,192,190,216the atoms involved for each of the torsions you wish to calculateREFERENCE32=0the reference values for each of the torsional anglesATOMS33=216,215,213,239the atoms involved for each of the torsions you wish to calculateREFERENCE33=0the reference values for each of the torsional anglesATOMS34=239,238,236,261the atoms involved for each of the torsions you wish to calculateREFERENCE34=0the reference values for each of the torsional anglesLABEL=alpha_d_minus ... ALPHABETAa label for the action so that its output can be referenced in the input to other actions
#alphaD- trans The ALPHABETA action with label alpha_d_minus calculates the following quantities:
Quantity Description alpha_d_minus.value the alpha beta CV ALPHABETA...Calculate the alpha beta CV More detailsATOMS1=24,4,3,1the atoms involved for each of the torsions you wish to calculateREFERENCE1=-1.57the reference values for each of the torsional anglesATOMS2=1,32,31,29the atoms involved for each of the torsions you wish to calculateREFERENCE2=-1.57the reference values for each of the torsional anglesATOMS3=29,55,54,52the atoms involved for each of the torsions you wish to calculateREFERENCE3=-1.57the reference values for each of the torsional anglesATOMS4=52,78,77,75the atoms involved for each of the torsions you wish to calculateREFERENCE4=-1.57the reference values for each of the torsional anglesATOMS5=75,101,100,98the atoms involved for each of the torsions you wish to calculateREFERENCE5=-1.57the reference values for each of the torsional anglesATOMS6=98,124,123,121the atoms involved for each of the torsions you wish to calculateREFERENCE6=-1.57the reference values for each of the torsional anglesATOMS7=121,147,146,144the atoms involved for each of the torsions you wish to calculateREFERENCE7=-1.57the reference values for each of the torsional anglesATOMS8=144,170,169,167the atoms involved for each of the torsions you wish to calculateREFERENCE8=-1.57the reference values for each of the torsional anglesATOMS9=167,193,192,190the atoms involved for each of the torsions you wish to calculateREFERENCE9=-1.57the reference values for each of the torsional anglesATOMS10=190,216,215,213the atoms involved for each of the torsions you wish to calculateREFERENCE10=-1.57the reference values for each of the torsional anglesATOMS11=213,239,238,236the atoms involved for each of the torsions you wish to calculateREFERENCE11=-1.57the reference values for each of the torsional anglesATOMS12=26,24,4,3the atoms involved for each of the torsions you wish to calculateREFERENCE12=3.14the reference values for each of the torsional anglesATOMS13=3,1,32,31the atoms involved for each of the torsions you wish to calculateREFERENCE13=3.14the reference values for each of the torsional anglesATOMS14=31,29,55,54the atoms involved for each of the torsions you wish to calculateREFERENCE14=3.14the reference values for each of the torsional anglesATOMS15=54,52,78,77the atoms involved for each of the torsions you wish to calculateREFERENCE15=3.14the reference values for each of the torsional anglesATOMS16=77,75,101,100the atoms involved for each of the torsions you wish to calculateREFERENCE16=3.14the reference values for each of the torsional anglesATOMS17=100,98,124,123the atoms involved for each of the torsions you wish to calculateREFERENCE17=3.14the reference values for each of the torsional anglesATOMS18=123,121,147,146the atoms involved for each of the torsions you wish to calculateREFERENCE18=3.14the reference values for each of the torsional anglesATOMS19=146,144,170,169the atoms involved for each of the torsions you wish to calculateREFERENCE19=3.14the reference values for each of the torsional anglesATOMS20=169,167,193,192the atoms involved for each of the torsions you wish to calculateREFERENCE20=3.14the reference values for each of the torsional anglesATOMS21=192,190,216,215the atoms involved for each of the torsions you wish to calculateREFERENCE21=3.14the reference values for each of the torsional anglesATOMS22=215,213,239,238the atoms involved for each of the torsions you wish to calculateREFERENCE22=3.14the reference values for each of the torsional anglesATOMS23=238,236,261,259the atoms involved for each of the torsions you wish to calculateREFERENCE23=3.14the reference values for each of the torsional anglesATOMS24=4,3,1,32the atoms involved for each of the torsions you wish to calculateREFERENCE24=3.14the reference values for each of the torsional anglesATOMS25=32,31,29,55the atoms involved for each of the torsions you wish to calculateREFERENCE25=3.14the reference values for each of the torsional anglesATOMS26=55,54,52,78the atoms involved for each of the torsions you wish to calculateREFERENCE26=3.14the reference values for each of the torsional anglesATOMS27=78,77,75,101the atoms involved for each of the torsions you wish to calculateREFERENCE27=3.14the reference values for each of the torsional anglesATOMS28=101,100,98,124the atoms involved for each of the torsions you wish to calculateREFERENCE28=3.14the reference values for each of the torsional anglesATOMS29=124,123,121,147the atoms involved for each of the torsions you wish to calculateREFERENCE29=3.14the reference values for each of the torsional anglesATOMS30=147,146,144,170the atoms involved for each of the torsions you wish to calculateREFERENCE30=3.14the reference values for each of the torsional anglesATOMS31=170,169,167,193the atoms involved for each of the torsions you wish to calculateREFERENCE31=3.14the reference values for each of the torsional anglesATOMS32=193,192,190,216the atoms involved for each of the torsions you wish to calculateREFERENCE32=3.14the reference values for each of the torsional anglesATOMS33=216,215,213,239the atoms involved for each of the torsions you wish to calculateREFERENCE33=3.14the reference values for each of the torsional anglesATOMS34=239,238,236,261the atoms involved for each of the torsions you wish to calculateREFERENCE34=3.14the reference values for each of the torsional anglesLABEL=alpha_d_minus_trans ... ALPHABETAa label for the action so that its output can be referenced in the input to other actions
#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 CV ALPHABETA...Calculate the alpha beta CV More detailsATOMS1=24,4,3,1the atoms involved for each of the torsions you wish to calculateREFERENCE1=1.57the reference values for each of the torsional anglesATOMS2=1,32,31,29the atoms involved for each of the torsions you wish to calculateREFERENCE2=1.57the reference values for each of the torsional anglesATOMS3=29,55,54,52the atoms involved for each of the torsions you wish to calculateREFERENCE3=1.57the reference values for each of the torsional anglesATOMS4=52,78,77,75the atoms involved for each of the torsions you wish to calculateREFERENCE4=1.57the reference values for each of the torsional anglesATOMS5=75,101,100,98the atoms involved for each of the torsions you wish to calculateREFERENCE5=1.57the reference values for each of the torsional anglesATOMS6=98,124,123,121the atoms involved for each of the torsions you wish to calculateREFERENCE6=1.57the reference values for each of the torsional anglesATOMS7=121,147,146,144the atoms involved for each of the torsions you wish to calculateREFERENCE7=1.57the reference values for each of the torsional anglesATOMS8=144,170,169,167the atoms involved for each of the torsions you wish to calculateREFERENCE8=1.57the reference values for each of the torsional anglesATOMS9=167,193,192,190the atoms involved for each of the torsions you wish to calculateREFERENCE9=1.57the reference values for each of the torsional anglesATOMS10=190,216,215,213the atoms involved for each of the torsions you wish to calculateREFERENCE10=1.57the reference values for each of the torsional anglesATOMS11=213,239,238,236the atoms involved for each of the torsions you wish to calculateREFERENCE11=1.57the reference values for each of the torsional anglesATOMS12=26,24,4,3the atoms involved for each of the torsions you wish to calculateREFERENCE12=3.14the reference values for each of the torsional anglesATOMS13=3,1,32,31the atoms involved for each of the torsions you wish to calculateREFERENCE13=3.14the reference values for each of the torsional anglesATOMS14=31,29,55,54the atoms involved for each of the torsions you wish to calculateREFERENCE14=3.14the reference values for each of the torsional anglesATOMS15=54,52,78,77the atoms involved for each of the torsions you wish to calculateREFERENCE15=3.14the reference values for each of the torsional anglesATOMS16=77,75,101,100the atoms involved for each of the torsions you wish to calculateREFERENCE16=3.14the reference values for each of the torsional anglesATOMS17=100,98,124,123the atoms involved for each of the torsions you wish to calculateREFERENCE17=3.14the reference values for each of the torsional anglesATOMS18=123,121,147,146the atoms involved for each of the torsions you wish to calculateREFERENCE18=3.14the reference values for each of the torsional anglesATOMS19=146,144,170,169the atoms involved for each of the torsions you wish to calculateREFERENCE19=3.14the reference values for each of the torsional anglesATOMS20=169,167,193,192the atoms involved for each of the torsions you wish to calculateREFERENCE20=3.14the reference values for each of the torsional anglesATOMS21=192,190,216,215the atoms involved for each of the torsions you wish to calculateREFERENCE21=3.14the reference values for each of the torsional anglesATOMS22=215,213,239,238the atoms involved for each of the torsions you wish to calculateREFERENCE22=3.14the reference values for each of the torsional anglesATOMS23=238,236,261,259the atoms involved for each of the torsions you wish to calculateREFERENCE23=3.14the reference values for each of the torsional anglesATOMS24=4,3,1,32the atoms involved for each of the torsions you wish to calculateREFERENCE24=0the reference values for each of the torsional anglesATOMS25=32,31,29,55the atoms involved for each of the torsions you wish to calculateREFERENCE25=0the reference values for each of the torsional anglesATOMS26=55,54,52,78the atoms involved for each of the torsions you wish to calculateREFERENCE26=0the reference values for each of the torsional anglesATOMS27=78,77,75,101the atoms involved for each of the torsions you wish to calculateREFERENCE27=0the reference values for each of the torsional anglesATOMS28=101,100,98,124the atoms involved for each of the torsions you wish to calculateREFERENCE28=0the reference values for each of the torsional anglesATOMS29=124,123,121,147the atoms involved for each of the torsions you wish to calculateREFERENCE29=0the reference values for each of the torsional anglesATOMS30=147,146,144,170the atoms involved for each of the torsions you wish to calculateREFERENCE30=0the reference values for each of the torsional anglesATOMS31=170,169,167,193the atoms involved for each of the torsions you wish to calculateREFERENCE31=0the reference values for each of the torsional anglesATOMS32=193,192,190,216the atoms involved for each of the torsions you wish to calculateREFERENCE32=0the reference values for each of the torsional anglesATOMS33=216,215,213,239the atoms involved for each of the torsions you wish to calculateREFERENCE33=0the reference values for each of the torsional anglesATOMS34=239,238,236,261the atoms involved for each of the torsions you wish to calculateREFERENCE34=0the reference values for each of the torsional anglesLABEL=alpha_d_plus ... ALPHABETAa label for the action so that its output can be referenced in the input to other actions
#alphaD+ trans The ALPHABETA action with label alpha_d_plus calculates the following quantities:
Quantity Description alpha_d_plus.value the alpha beta CV ALPHABETA...Calculate the alpha beta CV More detailsATOMS1=24,4,3,1the atoms involved for each of the torsions you wish to calculateREFERENCE1=1.57the reference values for each of the torsional anglesATOMS2=1,32,31,29the atoms involved for each of the torsions you wish to calculateREFERENCE2=1.57the reference values for each of the torsional anglesATOMS3=29,55,54,52the atoms involved for each of the torsions you wish to calculateREFERENCE3=1.57the reference values for each of the torsional anglesATOMS4=52,78,77,75the atoms involved for each of the torsions you wish to calculateREFERENCE4=1.57the reference values for each of the torsional anglesATOMS5=75,101,100,98the atoms involved for each of the torsions you wish to calculateREFERENCE5=1.57the reference values for each of the torsional anglesATOMS6=98,124,123,121the atoms involved for each of the torsions you wish to calculateREFERENCE6=1.57the reference values for each of the torsional anglesATOMS7=121,147,146,144the atoms involved for each of the torsions you wish to calculateREFERENCE7=1.57the reference values for each of the torsional anglesATOMS8=144,170,169,167the atoms involved for each of the torsions you wish to calculateREFERENCE8=1.57the reference values for each of the torsional anglesATOMS9=167,193,192,190the atoms involved for each of the torsions you wish to calculateREFERENCE9=1.57the reference values for each of the torsional anglesATOMS10=190,216,215,213the atoms involved for each of the torsions you wish to calculateREFERENCE10=1.57the reference values for each of the torsional anglesATOMS11=213,239,238,236the atoms involved for each of the torsions you wish to calculateREFERENCE11=1.57the reference values for each of the torsional anglesATOMS12=26,24,4,3the atoms involved for each of the torsions you wish to calculateREFERENCE12=3.14the reference values for each of the torsional anglesATOMS13=3,1,32,31the atoms involved for each of the torsions you wish to calculateREFERENCE13=3.14the reference values for each of the torsional anglesATOMS14=31,29,55,54the atoms involved for each of the torsions you wish to calculateREFERENCE14=3.14the reference values for each of the torsional anglesATOMS15=54,52,78,77the atoms involved for each of the torsions you wish to calculateREFERENCE15=3.14the reference values for each of the torsional anglesATOMS16=77,75,101,100the atoms involved for each of the torsions you wish to calculateREFERENCE16=3.14the reference values for each of the torsional anglesATOMS17=100,98,124,123the atoms involved for each of the torsions you wish to calculateREFERENCE17=3.14the reference values for each of the torsional anglesATOMS18=123,121,147,146the atoms involved for each of the torsions you wish to calculateREFERENCE18=3.14the reference values for each of the torsional anglesATOMS19=146,144,170,169the atoms involved for each of the torsions you wish to calculateREFERENCE19=3.14the reference values for each of the torsional anglesATOMS20=169,167,193,192the atoms involved for each of the torsions you wish to calculateREFERENCE20=3.14the reference values for each of the torsional anglesATOMS21=192,190,216,215the atoms involved for each of the torsions you wish to calculateREFERENCE21=3.14the reference values for each of the torsional anglesATOMS22=215,213,239,238the atoms involved for each of the torsions you wish to calculateREFERENCE22=3.14the reference values for each of the torsional anglesATOMS23=238,236,261,259the atoms involved for each of the torsions you wish to calculateREFERENCE23=3.14the reference values for each of the torsional anglesATOMS24=4,3,1,32the atoms involved for each of the torsions you wish to calculateREFERENCE24=3.14the reference values for each of the torsional anglesATOMS25=32,31,29,55the atoms involved for each of the torsions you wish to calculateREFERENCE25=3.14the reference values for each of the torsional anglesATOMS26=55,54,52,78the atoms involved for each of the torsions you wish to calculateREFERENCE26=3.14the reference values for each of the torsional anglesATOMS27=78,77,75,101the atoms involved for each of the torsions you wish to calculateREFERENCE27=3.14the reference values for each of the torsional anglesATOMS28=101,100,98,124the atoms involved for each of the torsions you wish to calculateREFERENCE28=3.14the reference values for each of the torsional anglesATOMS29=124,123,121,147the atoms involved for each of the torsions you wish to calculateREFERENCE29=3.14the reference values for each of the torsional anglesATOMS30=147,146,144,170the atoms involved for each of the torsions you wish to calculateREFERENCE30=3.14the reference values for each of the torsional anglesATOMS31=170,169,167,193the atoms involved for each of the torsions you wish to calculateREFERENCE31=3.14the reference values for each of the torsional anglesATOMS32=193,192,190,216the atoms involved for each of the torsions you wish to calculateREFERENCE32=3.14the reference values for each of the torsional anglesATOMS33=216,215,213,239the atoms involved for each of the torsions you wish to calculateREFERENCE33=3.14the reference values for each of the torsional anglesATOMS34=239,238,236,261the atoms involved for each of the torsions you wish to calculateREFERENCE34=3.14the reference values for each of the torsional anglesLABEL=alpha_d_plus_trans ... ALPHABETAa label for the action so that its output can be referenced in the input to other actions
# 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 CV ALPHABETA...Calculate the alpha beta CV More detailsATOMS1=24,4,3,1the atoms involved for each of the torsions you wish to calculateREFERENCE1=0.87the reference values for each of the torsional anglesATOMS2=1,32,31,29the atoms involved for each of the torsions you wish to calculateREFERENCE2=0.87the reference values for each of the torsional anglesATOMS3=29,55,54,52the atoms involved for each of the torsions you wish to calculateREFERENCE3=0.87the reference values for each of the torsional anglesATOMS4=52,78,77,75the atoms involved for each of the torsions you wish to calculateREFERENCE4=0.87the reference values for each of the torsional anglesATOMS5=75,101,100,98the atoms involved for each of the torsions you wish to calculateREFERENCE5=0.87the reference values for each of the torsional anglesATOMS6=98,124,123,121the atoms involved for each of the torsions you wish to calculateREFERENCE6=0.87the reference values for each of the torsional anglesATOMS7=121,147,146,144the atoms involved for each of the torsions you wish to calculateREFERENCE7=0.87the reference values for each of the torsional anglesATOMS8=144,170,169,167the atoms involved for each of the torsions you wish to calculateREFERENCE8=0.87the reference values for each of the torsional anglesATOMS9=167,193,192,190the atoms involved for each of the torsions you wish to calculateREFERENCE9=0.87the reference values for each of the torsional anglesATOMS10=190,216,215,213the atoms involved for each of the torsions you wish to calculateREFERENCE10=0.87the reference values for each of the torsional anglesATOMS11=213,239,238,236the atoms involved for each of the torsions you wish to calculateREFERENCE11=0.87the reference values for each of the torsional anglesATOMS12=26,24,4,3the atoms involved for each of the torsions you wish to calculateREFERENCE12=1.0the reference values for each of the torsional anglesATOMS13=3,1,32,31the atoms involved for each of the torsions you wish to calculateREFERENCE13=1.0the reference values for each of the torsional anglesATOMS14=31,29,55,54the atoms involved for each of the torsions you wish to calculateREFERENCE14=1.0the reference values for each of the torsional anglesATOMS15=54,52,78,77the atoms involved for each of the torsions you wish to calculateREFERENCE15=1.0the reference values for each of the torsional anglesATOMS16=77,75,101,100the atoms involved for each of the torsions you wish to calculateREFERENCE16=1.0the reference values for each of the torsional anglesATOMS17=100,98,124,123the atoms involved for each of the torsions you wish to calculateREFERENCE17=1.0the reference values for each of the torsional anglesATOMS18=123,121,147,146the atoms involved for each of the torsions you wish to calculateREFERENCE18=1.0the reference values for each of the torsional anglesATOMS19=146,144,170,169the atoms involved for each of the torsions you wish to calculateREFERENCE19=1.0the reference values for each of the torsional anglesATOMS20=169,167,193,192the atoms involved for each of the torsions you wish to calculateREFERENCE20=1.0the reference values for each of the torsional anglesATOMS21=192,190,216,215the atoms involved for each of the torsions you wish to calculateREFERENCE21=1.0the reference values for each of the torsional anglesATOMS22=215,213,239,238the atoms involved for each of the torsions you wish to calculateREFERENCE22=1.0the reference values for each of the torsional anglesATOMS23=238,236,261,259the atoms involved for each of the torsions you wish to calculateREFERENCE23=1.0the reference values for each of the torsional anglesATOMS24=4,3,1,32the atoms involved for each of the torsions you wish to calculateREFERENCE24=0the reference values for each of the torsional anglesATOMS25=32,31,29,55the atoms involved for each of the torsions you wish to calculateREFERENCE25=0the reference values for each of the torsional anglesATOMS26=55,54,52,78the atoms involved for each of the torsions you wish to calculateREFERENCE26=0the reference values for each of the torsional anglesATOMS27=78,77,75,101the atoms involved for each of the torsions you wish to calculateREFERENCE27=0the reference values for each of the torsional anglesATOMS28=101,100,98,124the atoms involved for each of the torsions you wish to calculateREFERENCE28=0the reference values for each of the torsional anglesATOMS29=124,123,121,147the atoms involved for each of the torsions you wish to calculateREFERENCE29=0the reference values for each of the torsional anglesATOMS30=147,146,144,170the atoms involved for each of the torsions you wish to calculateREFERENCE30=0the reference values for each of the torsional anglesATOMS31=170,169,167,193the atoms involved for each of the torsions you wish to calculateREFERENCE31=0the reference values for each of the torsional anglesATOMS32=193,192,190,216the atoms involved for each of the torsions you wish to calculateREFERENCE32=0the reference values for each of the torsional anglesATOMS33=216,215,213,239the atoms involved for each of the torsions you wish to calculateREFERENCE33=0the reference values for each of the torsional anglesATOMS34=239,238,236,261the atoms involved for each of the torsions you wish to calculateREFERENCE34=0the reference values for each of the torsional anglesLABEL=alpha_plus ... ALPHABETAa label for the action so that its output can be referenced in the input to other actions
# alpha+ trans The ALPHABETA action with label alpha_plus calculates the following quantities:
Quantity Description alpha_plus.value the alpha beta CV ALPHABETA...Calculate the alpha beta CV More detailsATOMS1=24,4,3,1the atoms involved for each of the torsions you wish to calculateREFERENCE1=0.87the reference values for each of the torsional anglesATOMS2=1,32,31,29the atoms involved for each of the torsions you wish to calculateREFERENCE2=0.87the reference values for each of the torsional anglesATOMS3=29,55,54,52the atoms involved for each of the torsions you wish to calculateREFERENCE3=0.87the reference values for each of the torsional anglesATOMS4=52,78,77,75the atoms involved for each of the torsions you wish to calculateREFERENCE4=0.87the reference values for each of the torsional anglesATOMS5=75,101,100,98the atoms involved for each of the torsions you wish to calculateREFERENCE5=0.87the reference values for each of the torsional anglesATOMS6=98,124,123,121the atoms involved for each of the torsions you wish to calculateREFERENCE6=0.87the reference values for each of the torsional anglesATOMS7=121,147,146,144the atoms involved for each of the torsions you wish to calculateREFERENCE7=0.87the reference values for each of the torsional anglesATOMS8=144,170,169,167the atoms involved for each of the torsions you wish to calculateREFERENCE8=0.87the reference values for each of the torsional anglesATOMS9=167,193,192,190the atoms involved for each of the torsions you wish to calculateREFERENCE9=0.87the reference values for each of the torsional anglesATOMS10=190,216,215,213the atoms involved for each of the torsions you wish to calculateREFERENCE10=0.87the reference values for each of the torsional anglesATOMS11=213,239,238,236the atoms involved for each of the torsions you wish to calculateREFERENCE11=0.87the reference values for each of the torsional anglesATOMS12=26,24,4,3the atoms involved for each of the torsions you wish to calculateREFERENCE12=1.0the reference values for each of the torsional anglesATOMS13=3,1,32,31the atoms involved for each of the torsions you wish to calculateREFERENCE13=1.0the reference values for each of the torsional anglesATOMS14=31,29,55,54the atoms involved for each of the torsions you wish to calculateREFERENCE14=1.0the reference values for each of the torsional anglesATOMS15=54,52,78,77the atoms involved for each of the torsions you wish to calculateREFERENCE15=1.0the reference values for each of the torsional anglesATOMS16=77,75,101,100the atoms involved for each of the torsions you wish to calculateREFERENCE16=1.0the reference values for each of the torsional anglesATOMS17=100,98,124,123the atoms involved for each of the torsions you wish to calculateREFERENCE17=1.0the reference values for each of the torsional anglesATOMS18=123,121,147,146the atoms involved for each of the torsions you wish to calculateREFERENCE18=1.0the reference values for each of the torsional anglesATOMS19=146,144,170,169the atoms involved for each of the torsions you wish to calculateREFERENCE19=1.0the reference values for each of the torsional anglesATOMS20=169,167,193,192the atoms involved for each of the torsions you wish to calculateREFERENCE20=1.0the reference values for each of the torsional anglesATOMS21=192,190,216,215the atoms involved for each of the torsions you wish to calculateREFERENCE21=1.0the reference values for each of the torsional anglesATOMS22=215,213,239,238the atoms involved for each of the torsions you wish to calculateREFERENCE22=1.0the reference values for each of the torsional anglesATOMS23=238,236,261,259the atoms involved for each of the torsions you wish to calculateREFERENCE23=1.0the reference values for each of the torsional anglesATOMS24=4,3,1,32the atoms involved for each of the torsions you wish to calculateREFERENCE24=3.14the reference values for each of the torsional anglesATOMS25=32,31,29,55the atoms involved for each of the torsions you wish to calculateREFERENCE25=3.14the reference values for each of the torsional anglesATOMS26=55,54,52,78the atoms involved for each of the torsions you wish to calculateREFERENCE26=3.14the reference values for each of the torsional anglesATOMS27=78,77,75,101the atoms involved for each of the torsions you wish to calculateREFERENCE27=3.14the reference values for each of the torsional anglesATOMS28=101,100,98,124the atoms involved for each of the torsions you wish to calculateREFERENCE28=3.14the reference values for each of the torsional anglesATOMS29=124,123,121,147the atoms involved for each of the torsions you wish to calculateREFERENCE29=3.14the reference values for each of the torsional anglesATOMS30=147,146,144,170the atoms involved for each of the torsions you wish to calculateREFERENCE30=3.14the reference values for each of the torsional anglesATOMS31=170,169,167,193the atoms involved for each of the torsions you wish to calculateREFERENCE31=3.14the reference values for each of the torsional anglesATOMS32=193,192,190,216the atoms involved for each of the torsions you wish to calculateREFERENCE32=3.14the reference values for each of the torsional anglesATOMS33=216,215,213,239the atoms involved for each of the torsions you wish to calculateREFERENCE33=3.14the reference values for each of the torsional anglesATOMS34=239,238,236,261the atoms involved for each of the torsions you wish to calculateREFERENCE34=3.14the reference values for each of the torsional anglesLABEL=alpha_plus_trans ... ALPHABETAa label for the action so that its output can be referenced in the input to other actions
# alpha- cis The ALPHABETA action with label alpha_plus_trans calculates the following quantities:
Quantity Description alpha_plus_trans.value the alpha beta CV ALPHABETA...Calculate the alpha beta CV More detailsATOMS1=24,4,3,1the atoms involved for each of the torsions you wish to calculateREFERENCE1=-0.87the reference values for each of the torsional anglesATOMS2=1,32,31,29the atoms involved for each of the torsions you wish to calculateREFERENCE2=-0.87the reference values for each of the torsional anglesATOMS3=29,55,54,52the atoms involved for each of the torsions you wish to calculateREFERENCE3=-0.87the reference values for each of the torsional anglesATOMS4=52,78,77,75the atoms involved for each of the torsions you wish to calculateREFERENCE4=-0.87the reference values for each of the torsional anglesATOMS5=75,101,100,98the atoms involved for each of the torsions you wish to calculateREFERENCE5=-0.87the reference values for each of the torsional anglesATOMS6=98,124,123,121the atoms involved for each of the torsions you wish to calculateREFERENCE6=-0.87the reference values for each of the torsional anglesATOMS7=121,147,146,144the atoms involved for each of the torsions you wish to calculateREFERENCE7=-0.87the reference values for each of the torsional anglesATOMS8=144,170,169,167the atoms involved for each of the torsions you wish to calculateREFERENCE8=-0.87the reference values for each of the torsional anglesATOMS9=167,193,192,190the atoms involved for each of the torsions you wish to calculateREFERENCE9=-0.87the reference values for each of the torsional anglesATOMS10=190,216,215,213the atoms involved for each of the torsions you wish to calculateREFERENCE10=-0.87the reference values for each of the torsional anglesATOMS11=213,239,238,236the atoms involved for each of the torsions you wish to calculateREFERENCE11=-0.87the reference values for each of the torsional anglesATOMS12=26,24,4,3the atoms involved for each of the torsions you wish to calculateREFERENCE12=-1.0the reference values for each of the torsional anglesATOMS13=3,1,32,31the atoms involved for each of the torsions you wish to calculateREFERENCE13=-1.0the reference values for each of the torsional anglesATOMS14=31,29,55,54the atoms involved for each of the torsions you wish to calculateREFERENCE14=-1.0the reference values for each of the torsional anglesATOMS15=54,52,78,77the atoms involved for each of the torsions you wish to calculateREFERENCE15=-1.0the reference values for each of the torsional anglesATOMS16=77,75,101,100the atoms involved for each of the torsions you wish to calculateREFERENCE16=-1.0the reference values for each of the torsional anglesATOMS17=100,98,124,123the atoms involved for each of the torsions you wish to calculateREFERENCE17=-1.0the reference values for each of the torsional anglesATOMS18=123,121,147,146the atoms involved for each of the torsions you wish to calculateREFERENCE18=-1.0the reference values for each of the torsional anglesATOMS19=146,144,170,169the atoms involved for each of the torsions you wish to calculateREFERENCE19=-1.0the reference values for each of the torsional anglesATOMS20=169,167,193,192the atoms involved for each of the torsions you wish to calculateREFERENCE20=-1.0the reference values for each of the torsional anglesATOMS21=192,190,216,215the atoms involved for each of the torsions you wish to calculateREFERENCE21=-1.0the reference values for each of the torsional anglesATOMS22=215,213,239,238the atoms involved for each of the torsions you wish to calculateREFERENCE22=-1.0the reference values for each of the torsional anglesATOMS23=238,236,261,259the atoms involved for each of the torsions you wish to calculateREFERENCE23=-1.0the reference values for each of the torsional anglesATOMS24=4,3,1,32the atoms involved for each of the torsions you wish to calculateREFERENCE24=0the reference values for each of the torsional anglesATOMS25=32,31,29,55the atoms involved for each of the torsions you wish to calculateREFERENCE25=0the reference values for each of the torsional anglesATOMS26=55,54,52,78the atoms involved for each of the torsions you wish to calculateREFERENCE26=0the reference values for each of the torsional anglesATOMS27=78,77,75,101the atoms involved for each of the torsions you wish to calculateREFERENCE27=0the reference values for each of the torsional anglesATOMS28=101,100,98,124the atoms involved for each of the torsions you wish to calculateREFERENCE28=0the reference values for each of the torsional anglesATOMS29=124,123,121,147the atoms involved for each of the torsions you wish to calculateREFERENCE29=0the reference values for each of the torsional anglesATOMS30=147,146,144,170the atoms involved for each of the torsions you wish to calculateREFERENCE30=0the reference values for each of the torsional anglesATOMS31=170,169,167,193the atoms involved for each of the torsions you wish to calculateREFERENCE31=0the reference values for each of the torsional anglesATOMS32=193,192,190,216the atoms involved for each of the torsions you wish to calculateREFERENCE32=0the reference values for each of the torsional anglesATOMS33=216,215,213,239the atoms involved for each of the torsions you wish to calculateREFERENCE33=0the reference values for each of the torsional anglesATOMS34=239,238,236,261the atoms involved for each of the torsions you wish to calculateREFERENCE34=0the reference values for each of the torsional anglesLABEL=alpha_minus ... ALPHABETAa label for the action so that its output can be referenced in the input to other actions
# alpha- trans The ALPHABETA action with label alpha_minus calculates the following quantities:
Quantity Description alpha_minus.value the alpha beta CV ALPHABETA...Calculate the alpha beta CV More detailsATOMS1=24,4,3,1the atoms involved for each of the torsions you wish to calculateREFERENCE1=-0.87the reference values for each of the torsional anglesATOMS2=1,32,31,29the atoms involved for each of the torsions you wish to calculateREFERENCE2=-0.87the reference values for each of the torsional anglesATOMS3=29,55,54,52the atoms involved for each of the torsions you wish to calculateREFERENCE3=-0.87the reference values for each of the torsional anglesATOMS4=52,78,77,75the atoms involved for each of the torsions you wish to calculateREFERENCE4=-0.87the reference values for each of the torsional anglesATOMS5=75,101,100,98the atoms involved for each of the torsions you wish to calculateREFERENCE5=-0.87the reference values for each of the torsional anglesATOMS6=98,124,123,121the atoms involved for each of the torsions you wish to calculateREFERENCE6=-0.87the reference values for each of the torsional anglesATOMS7=121,147,146,144the atoms involved for each of the torsions you wish to calculateREFERENCE7=-0.87the reference values for each of the torsional anglesATOMS8=144,170,169,167the atoms involved for each of the torsions you wish to calculateREFERENCE8=-0.87the reference values for each of the torsional anglesATOMS9=167,193,192,190the atoms involved for each of the torsions you wish to calculateREFERENCE9=-0.87the reference values for each of the torsional anglesATOMS10=190,216,215,213the atoms involved for each of the torsions you wish to calculateREFERENCE10=-0.87the reference values for each of the torsional anglesATOMS11=213,239,238,236the atoms involved for each of the torsions you wish to calculateREFERENCE11=-0.87the reference values for each of the torsional anglesATOMS12=26,24,4,3the atoms involved for each of the torsions you wish to calculateREFERENCE12=-1.0the reference values for each of the torsional anglesATOMS13=3,1,32,31the atoms involved for each of the torsions you wish to calculateREFERENCE13=-1.0the reference values for each of the torsional anglesATOMS14=31,29,55,54the atoms involved for each of the torsions you wish to calculateREFERENCE14=-1.0the reference values for each of the torsional anglesATOMS15=54,52,78,77the atoms involved for each of the torsions you wish to calculateREFERENCE15=-1.0the reference values for each of the torsional anglesATOMS16=77,75,101,100the atoms involved for each of the torsions you wish to calculateREFERENCE16=-1.0the reference values for each of the torsional anglesATOMS17=100,98,124,123the atoms involved for each of the torsions you wish to calculateREFERENCE17=-1.0the reference values for each of the torsional anglesATOMS18=123,121,147,146the atoms involved for each of the torsions you wish to calculateREFERENCE18=-1.0the reference values for each of the torsional anglesATOMS19=146,144,170,169the atoms involved for each of the torsions you wish to calculateREFERENCE19=-1.0the reference values for each of the torsional anglesATOMS20=169,167,193,192the atoms involved for each of the torsions you wish to calculateREFERENCE20=-1.0the reference values for each of the torsional anglesATOMS21=192,190,216,215the atoms involved for each of the torsions you wish to calculateREFERENCE21=-1.0the reference values for each of the torsional anglesATOMS22=215,213,239,238the atoms involved for each of the torsions you wish to calculateREFERENCE22=-1.0the reference values for each of the torsional anglesATOMS23=238,236,261,259the atoms involved for each of the torsions you wish to calculateREFERENCE23=-1.0the reference values for each of the torsional anglesATOMS24=4,3,1,32the atoms involved for each of the torsions you wish to calculateREFERENCE24=3.14the reference values for each of the torsional anglesATOMS25=32,31,29,55the atoms involved for each of the torsions you wish to calculateREFERENCE25=3.14the reference values for each of the torsional anglesATOMS26=55,54,52,78the atoms involved for each of the torsions you wish to calculateREFERENCE26=3.14the reference values for each of the torsional anglesATOMS27=78,77,75,101the atoms involved for each of the torsions you wish to calculateREFERENCE27=3.14the reference values for each of the torsional anglesATOMS28=101,100,98,124the atoms involved for each of the torsions you wish to calculateREFERENCE28=3.14the reference values for each of the torsional anglesATOMS29=124,123,121,147the atoms involved for each of the torsions you wish to calculateREFERENCE29=3.14the reference values for each of the torsional anglesATOMS30=147,146,144,170the atoms involved for each of the torsions you wish to calculateREFERENCE30=3.14the reference values for each of the torsional anglesATOMS31=170,169,167,193the atoms involved for each of the torsions you wish to calculateREFERENCE31=3.14the reference values for each of the torsional anglesATOMS32=193,192,190,216the atoms involved for each of the torsions you wish to calculateREFERENCE32=3.14the reference values for each of the torsional anglesATOMS33=216,215,213,239the atoms involved for each of the torsions you wish to calculateREFERENCE33=3.14the reference values for each of the torsional anglesATOMS34=239,238,236,261the atoms involved for each of the torsions you wish to calculateREFERENCE34=3.14the reference values for each of the torsional anglesLABEL=alpha_minus_trans ... ALPHABETAa label for the action so that its output can be referenced in the input to other actions
#c7beta+ cis The ALPHABETA action with label alpha_minus_trans calculates the following quantities:
Quantity Description alpha_minus_trans.value the alpha beta CV ALPHABETA...Calculate the alpha beta CV More detailsATOMS1=24,4,3,1the atoms involved for each of the torsions you wish to calculateREFERENCE1=2.09the reference values for each of the torsional anglesATOMS2=1,32,31,29the atoms involved for each of the torsions you wish to calculateREFERENCE2=2.09the reference values for each of the torsional anglesATOMS3=29,55,54,52the atoms involved for each of the torsions you wish to calculateREFERENCE3=2.09the reference values for each of the torsional anglesATOMS4=52,78,77,75the atoms involved for each of the torsions you wish to calculateREFERENCE4=2.09the reference values for each of the torsional anglesATOMS5=75,101,100,98the atoms involved for each of the torsions you wish to calculateREFERENCE5=2.09the reference values for each of the torsional anglesATOMS6=98,124,123,121the atoms involved for each of the torsions you wish to calculateREFERENCE6=2.09the reference values for each of the torsional anglesATOMS7=121,147,146,144the atoms involved for each of the torsions you wish to calculateREFERENCE7=2.09the reference values for each of the torsional anglesATOMS8=144,170,169,167the atoms involved for each of the torsions you wish to calculateREFERENCE8=2.09the reference values for each of the torsional anglesATOMS9=167,193,192,190the atoms involved for each of the torsions you wish to calculateREFERENCE9=2.09the reference values for each of the torsional anglesATOMS10=190,216,215,213the atoms involved for each of the torsions you wish to calculateREFERENCE10=2.09the reference values for each of the torsional anglesATOMS11=213,239,238,236the atoms involved for each of the torsions you wish to calculateREFERENCE11=2.09the reference values for each of the torsional anglesATOMS12=26,24,4,3the atoms involved for each of the torsions you wish to calculateREFERENCE12=-1.3the reference values for each of the torsional anglesATOMS13=3,1,32,31the atoms involved for each of the torsions you wish to calculateREFERENCE13=-1.3the reference values for each of the torsional anglesATOMS14=31,29,55,54the atoms involved for each of the torsions you wish to calculateREFERENCE14=-1.3the reference values for each of the torsional anglesATOMS15=54,52,78,77the atoms involved for each of the torsions you wish to calculateREFERENCE15=-1.3the reference values for each of the torsional anglesATOMS16=77,75,101,100the atoms involved for each of the torsions you wish to calculateREFERENCE16=-1.3the reference values for each of the torsional anglesATOMS17=100,98,124,123the atoms involved for each of the torsions you wish to calculateREFERENCE17=-1.3the reference values for each of the torsional anglesATOMS18=123,121,147,146the atoms involved for each of the torsions you wish to calculateREFERENCE18=-1.3the reference values for each of the torsional anglesATOMS19=146,144,170,169the atoms involved for each of the torsions you wish to calculateREFERENCE19=-1.3the reference values for each of the torsional anglesATOMS20=169,167,193,192the atoms involved for each of the torsions you wish to calculateREFERENCE20=-1.3the reference values for each of the torsional anglesATOMS21=192,190,216,215the atoms involved for each of the torsions you wish to calculateREFERENCE21=-1.3the reference values for each of the torsional anglesATOMS22=215,213,239,238the atoms involved for each of the torsions you wish to calculateREFERENCE22=-1.3the reference values for each of the torsional anglesATOMS23=238,236,261,259the atoms involved for each of the torsions you wish to calculateREFERENCE23=-1.3the reference values for each of the torsional anglesATOMS24=4,3,1,32the atoms involved for each of the torsions you wish to calculateREFERENCE24=0the reference values for each of the torsional anglesATOMS25=32,31,29,55the atoms involved for each of the torsions you wish to calculateREFERENCE25=0the reference values for each of the torsional anglesATOMS26=55,54,52,78the atoms involved for each of the torsions you wish to calculateREFERENCE26=0the reference values for each of the torsional anglesATOMS27=78,77,75,101the atoms involved for each of the torsions you wish to calculateREFERENCE27=0the reference values for each of the torsional anglesATOMS28=101,100,98,124the atoms involved for each of the torsions you wish to calculateREFERENCE28=0the reference values for each of the torsional anglesATOMS29=124,123,121,147the atoms involved for each of the torsions you wish to calculateREFERENCE29=0the reference values for each of the torsional anglesATOMS30=147,146,144,170the atoms involved for each of the torsions you wish to calculateREFERENCE30=0the reference values for each of the torsional anglesATOMS31=170,169,167,193the atoms involved for each of the torsions you wish to calculateREFERENCE31=0the reference values for each of the torsional anglesATOMS32=193,192,190,216the atoms involved for each of the torsions you wish to calculateREFERENCE32=0the reference values for each of the torsional anglesATOMS33=216,215,213,239the atoms involved for each of the torsions you wish to calculateREFERENCE33=0the reference values for each of the torsional anglesATOMS34=239,238,236,261the atoms involved for each of the torsions you wish to calculateREFERENCE34=0the reference values for each of the torsional anglesLABEL=c7beta_plus ... ALPHABETAa label for the action so that its output can be referenced in the input to other actions
#c7beta+ trans The ALPHABETA action with label c7beta_plus calculates the following quantities:
Quantity Description c7beta_plus.value the alpha beta CV ALPHABETA...Calculate the alpha beta CV More detailsATOMS1=24,4,3,1the atoms involved for each of the torsions you wish to calculateREFERENCE1=2.09the reference values for each of the torsional anglesATOMS2=1,32,31,29the atoms involved for each of the torsions you wish to calculateREFERENCE2=2.09the reference values for each of the torsional anglesATOMS3=29,55,54,52the atoms involved for each of the torsions you wish to calculateREFERENCE3=2.09the reference values for each of the torsional anglesATOMS4=52,78,77,75the atoms involved for each of the torsions you wish to calculateREFERENCE4=2.09the reference values for each of the torsional anglesATOMS5=75,101,100,98the atoms involved for each of the torsions you wish to calculateREFERENCE5=2.09the reference values for each of the torsional anglesATOMS6=98,124,123,121the atoms involved for each of the torsions you wish to calculateREFERENCE6=2.09the reference values for each of the torsional anglesATOMS7=121,147,146,144the atoms involved for each of the torsions you wish to calculateREFERENCE7=2.09the reference values for each of the torsional anglesATOMS8=144,170,169,167the atoms involved for each of the torsions you wish to calculateREFERENCE8=2.09the reference values for each of the torsional anglesATOMS9=167,193,192,190the atoms involved for each of the torsions you wish to calculateREFERENCE9=2.09the reference values for each of the torsional anglesATOMS10=190,216,215,213the atoms involved for each of the torsions you wish to calculateREFERENCE10=2.09the reference values for each of the torsional anglesATOMS11=213,239,238,236the atoms involved for each of the torsions you wish to calculateREFERENCE11=2.09the reference values for each of the torsional anglesATOMS12=26,24,4,3the atoms involved for each of the torsions you wish to calculateREFERENCE12=-1.3the reference values for each of the torsional anglesATOMS13=3,1,32,31the atoms involved for each of the torsions you wish to calculateREFERENCE13=-1.3the reference values for each of the torsional anglesATOMS14=31,29,55,54the atoms involved for each of the torsions you wish to calculateREFERENCE14=-1.3the reference values for each of the torsional anglesATOMS15=54,52,78,77the atoms involved for each of the torsions you wish to calculateREFERENCE15=-1.3the reference values for each of the torsional anglesATOMS16=77,75,101,100the atoms involved for each of the torsions you wish to calculateREFERENCE16=-1.3the reference values for each of the torsional anglesATOMS17=100,98,124,123the atoms involved for each of the torsions you wish to calculateREFERENCE17=-1.3the reference values for each of the torsional anglesATOMS18=123,121,147,146the atoms involved for each of the torsions you wish to calculateREFERENCE18=-1.3the reference values for each of the torsional anglesATOMS19=146,144,170,169the atoms involved for each of the torsions you wish to calculateREFERENCE19=-1.3the reference values for each of the torsional anglesATOMS20=169,167,193,192the atoms involved for each of the torsions you wish to calculateREFERENCE20=-1.3the reference values for each of the torsional anglesATOMS21=192,190,216,215the atoms involved for each of the torsions you wish to calculateREFERENCE21=-1.3the reference values for each of the torsional anglesATOMS22=215,213,239,238the atoms involved for each of the torsions you wish to calculateREFERENCE22=-1.3the reference values for each of the torsional anglesATOMS23=238,236,261,259the atoms involved for each of the torsions you wish to calculateREFERENCE23=-1.3the reference values for each of the torsional anglesATOMS24=4,3,1,32the atoms involved for each of the torsions you wish to calculateREFERENCE24=3.14the reference values for each of the torsional anglesATOMS25=32,31,29,55the atoms involved for each of the torsions you wish to calculateREFERENCE25=3.14the reference values for each of the torsional anglesATOMS26=55,54,52,78the atoms involved for each of the torsions you wish to calculateREFERENCE26=3.14the reference values for each of the torsional anglesATOMS27=78,77,75,101the atoms involved for each of the torsions you wish to calculateREFERENCE27=3.14the reference values for each of the torsional anglesATOMS28=101,100,98,124the atoms involved for each of the torsions you wish to calculateREFERENCE28=3.14the reference values for each of the torsional anglesATOMS29=124,123,121,147the atoms involved for each of the torsions you wish to calculateREFERENCE29=3.14the reference values for each of the torsional anglesATOMS30=147,146,144,170the atoms involved for each of the torsions you wish to calculateREFERENCE30=3.14the reference values for each of the torsional anglesATOMS31=170,169,167,193the atoms involved for each of the torsions you wish to calculateREFERENCE31=3.14the reference values for each of the torsional anglesATOMS32=193,192,190,216the atoms involved for each of the torsions you wish to calculateREFERENCE32=3.14the reference values for each of the torsional anglesATOMS33=216,215,213,239the atoms involved for each of the torsions you wish to calculateREFERENCE33=3.14the reference values for each of the torsional anglesATOMS34=239,238,236,261the atoms involved for each of the torsions you wish to calculateREFERENCE34=3.14the reference values for each of the torsional anglesLABEL=c7beta_plus_trans ... ALPHABETAa label for the action so that its output can be referenced in the input to other actions
#c7beta- cis The ALPHABETA action with label c7beta_plus_trans calculates the following quantities:
Quantity Description c7beta_plus_trans.value the alpha beta CV ALPHABETA...Calculate the alpha beta CV More detailsATOMS1=24,4,3,1the atoms involved for each of the torsions you wish to calculateREFERENCE1=-2.09the reference values for each of the torsional anglesATOMS2=1,32,31,29the atoms involved for each of the torsions you wish to calculateREFERENCE2=-2.09the reference values for each of the torsional anglesATOMS3=29,55,54,52the atoms involved for each of the torsions you wish to calculateREFERENCE3=-2.09the reference values for each of the torsional anglesATOMS4=52,78,77,75the atoms involved for each of the torsions you wish to calculateREFERENCE4=-2.09the reference values for each of the torsional anglesATOMS5=75,101,100,98the atoms involved for each of the torsions you wish to calculateREFERENCE5=-2.09the reference values for each of the torsional anglesATOMS6=98,124,123,121the atoms involved for each of the torsions you wish to calculateREFERENCE6=-2.09the reference values for each of the torsional anglesATOMS7=121,147,146,144the atoms involved for each of the torsions you wish to calculateREFERENCE7=-2.09the reference values for each of the torsional anglesATOMS8=144,170,169,167the atoms involved for each of the torsions you wish to calculateREFERENCE8=-2.09the reference values for each of the torsional anglesATOMS9=167,193,192,190the atoms involved for each of the torsions you wish to calculateREFERENCE9=-2.09the reference values for each of the torsional anglesATOMS10=190,216,215,213the atoms involved for each of the torsions you wish to calculateREFERENCE10=-2.09the reference values for each of the torsional anglesATOMS11=213,239,238,236the atoms involved for each of the torsions you wish to calculateREFERENCE11=-2.09the reference values for each of the torsional anglesATOMS12=26,24,4,3the atoms involved for each of the torsions you wish to calculateREFERENCE12=1.3the reference values for each of the torsional anglesATOMS13=3,1,32,31the atoms involved for each of the torsions you wish to calculateREFERENCE13=1.3the reference values for each of the torsional anglesATOMS14=31,29,55,54the atoms involved for each of the torsions you wish to calculateREFERENCE14=1.3the reference values for each of the torsional anglesATOMS15=54,52,78,77the atoms involved for each of the torsions you wish to calculateREFERENCE15=1.3the reference values for each of the torsional anglesATOMS16=77,75,101,100the atoms involved for each of the torsions you wish to calculateREFERENCE16=1.3the reference values for each of the torsional anglesATOMS17=100,98,124,123the atoms involved for each of the torsions you wish to calculateREFERENCE17=1.3the reference values for each of the torsional anglesATOMS18=123,121,147,146the atoms involved for each of the torsions you wish to calculateREFERENCE18=1.3the reference values for each of the torsional anglesATOMS19=146,144,170,169the atoms involved for each of the torsions you wish to calculateREFERENCE19=1.3the reference values for each of the torsional anglesATOMS20=169,167,193,192the atoms involved for each of the torsions you wish to calculateREFERENCE20=1.3the reference values for each of the torsional anglesATOMS21=192,190,216,215the atoms involved for each of the torsions you wish to calculateREFERENCE21=1.3the reference values for each of the torsional anglesATOMS22=215,213,239,238the atoms involved for each of the torsions you wish to calculateREFERENCE22=1.3the reference values for each of the torsional anglesATOMS23=238,236,261,259the atoms involved for each of the torsions you wish to calculateREFERENCE23=1.3the reference values for each of the torsional anglesATOMS24=4,3,1,32the atoms involved for each of the torsions you wish to calculateREFERENCE24=0the reference values for each of the torsional anglesATOMS25=32,31,29,55the atoms involved for each of the torsions you wish to calculateREFERENCE25=0the reference values for each of the torsional anglesATOMS26=55,54,52,78the atoms involved for each of the torsions you wish to calculateREFERENCE26=0the reference values for each of the torsional anglesATOMS27=78,77,75,101the atoms involved for each of the torsions you wish to calculateREFERENCE27=0the reference values for each of the torsional anglesATOMS28=101,100,98,124the atoms involved for each of the torsions you wish to calculateREFERENCE28=0the reference values for each of the torsional anglesATOMS29=124,123,121,147the atoms involved for each of the torsions you wish to calculateREFERENCE29=0the reference values for each of the torsional anglesATOMS30=147,146,144,170the atoms involved for each of the torsions you wish to calculateREFERENCE30=0the reference values for each of the torsional anglesATOMS31=170,169,167,193the atoms involved for each of the torsions you wish to calculateREFERENCE31=0the reference values for each of the torsional anglesATOMS32=193,192,190,216the atoms involved for each of the torsions you wish to calculateREFERENCE32=0the reference values for each of the torsional anglesATOMS33=216,215,213,239the atoms involved for each of the torsions you wish to calculateREFERENCE33=0the reference values for each of the torsional anglesATOMS34=239,238,236,261the atoms involved for each of the torsions you wish to calculateREFERENCE34=0the reference values for each of the torsional anglesLABEL=c7beta_minus ... ALPHABETAa label for the action so that its output can be referenced in the input to other actions
#c7beta+ trans The ALPHABETA action with label c7beta_minus calculates the following quantities:
Quantity Description c7beta_minus.value the alpha beta CV ALPHABETA...Calculate the alpha beta CV More detailsATOMS1=24,4,3,1the atoms involved for each of the torsions you wish to calculateREFERENCE1=-2.09the reference values for each of the torsional anglesATOMS2=1,32,31,29the atoms involved for each of the torsions you wish to calculateREFERENCE2=-2.09the reference values for each of the torsional anglesATOMS3=29,55,54,52the atoms involved for each of the torsions you wish to calculateREFERENCE3=-2.09the reference values for each of the torsional anglesATOMS4=52,78,77,75the atoms involved for each of the torsions you wish to calculateREFERENCE4=-2.09the reference values for each of the torsional anglesATOMS5=75,101,100,98the atoms involved for each of the torsions you wish to calculateREFERENCE5=-2.09the reference values for each of the torsional anglesATOMS6=98,124,123,121the atoms involved for each of the torsions you wish to calculateREFERENCE6=-2.09the reference values for each of the torsional anglesATOMS7=121,147,146,144the atoms involved for each of the torsions you wish to calculateREFERENCE7=-2.09the reference values for each of the torsional anglesATOMS8=144,170,169,167the atoms involved for each of the torsions you wish to calculateREFERENCE8=-2.09the reference values for each of the torsional anglesATOMS9=167,193,192,190the atoms involved for each of the torsions you wish to calculateREFERENCE9=-2.09the reference values for each of the torsional anglesATOMS10=190,216,215,213the atoms involved for each of the torsions you wish to calculateREFERENCE10=-2.09the reference values for each of the torsional anglesATOMS11=213,239,238,236the atoms involved for each of the torsions you wish to calculateREFERENCE11=-2.09the reference values for each of the torsional anglesATOMS12=26,24,4,3the atoms involved for each of the torsions you wish to calculateREFERENCE12=1.3the reference values for each of the torsional anglesATOMS13=3,1,32,31the atoms involved for each of the torsions you wish to calculateREFERENCE13=1.3the reference values for each of the torsional anglesATOMS14=31,29,55,54the atoms involved for each of the torsions you wish to calculateREFERENCE14=1.3the reference values for each of the torsional anglesATOMS15=54,52,78,77the atoms involved for each of the torsions you wish to calculateREFERENCE15=1.3the reference values for each of the torsional anglesATOMS16=77,75,101,100the atoms involved for each of the torsions you wish to calculateREFERENCE16=1.3the reference values for each of the torsional anglesATOMS17=100,98,124,123the atoms involved for each of the torsions you wish to calculateREFERENCE17=1.3the reference values for each of the torsional anglesATOMS18=123,121,147,146the atoms involved for each of the torsions you wish to calculateREFERENCE18=1.3the reference values for each of the torsional anglesATOMS19=146,144,170,169the atoms involved for each of the torsions you wish to calculateREFERENCE19=1.3the reference values for each of the torsional anglesATOMS20=169,167,193,192the atoms involved for each of the torsions you wish to calculateREFERENCE20=1.3the reference values for each of the torsional anglesATOMS21=192,190,216,215the atoms involved for each of the torsions you wish to calculateREFERENCE21=1.3the reference values for each of the torsional anglesATOMS22=215,213,239,238the atoms involved for each of the torsions you wish to calculateREFERENCE22=1.3the reference values for each of the torsional anglesATOMS23=238,236,261,259the atoms involved for each of the torsions you wish to calculateREFERENCE23=1.3the reference values for each of the torsional anglesATOMS24=4,3,1,32the atoms involved for each of the torsions you wish to calculateREFERENCE24=3.14the reference values for each of the torsional anglesATOMS25=32,31,29,55the atoms involved for each of the torsions you wish to calculateREFERENCE25=3.14the reference values for each of the torsional anglesATOMS26=55,54,52,78the atoms involved for each of the torsions you wish to calculateREFERENCE26=3.14the reference values for each of the torsional anglesATOMS27=78,77,75,101the atoms involved for each of the torsions you wish to calculateREFERENCE27=3.14the reference values for each of the torsional anglesATOMS28=101,100,98,124the atoms involved for each of the torsions you wish to calculateREFERENCE28=3.14the reference values for each of the torsional anglesATOMS29=124,123,121,147the atoms involved for each of the torsions you wish to calculateREFERENCE29=3.14the reference values for each of the torsional anglesATOMS30=147,146,144,170the atoms involved for each of the torsions you wish to calculateREFERENCE30=3.14the reference values for each of the torsional anglesATOMS31=170,169,167,193the atoms involved for each of the torsions you wish to calculateREFERENCE31=3.14the reference values for each of the torsional anglesATOMS32=193,192,190,216the atoms involved for each of the torsions you wish to calculateREFERENCE32=3.14the reference values for each of the torsional anglesATOMS33=216,215,213,239the atoms involved for each of the torsions you wish to calculateREFERENCE33=3.14the reference values for each of the torsional anglesATOMS34=239,238,236,261the atoms involved for each of the torsions you wish to calculateREFERENCE34=3.14the reference values for each of the torsional anglesLABEL=c7beta_minus_trans ... ALPHABETA # --- End of included input ---a label for the action so that its output can be referenced in the input to other actions
# WTE The ALPHABETA action with label c7beta_minus_trans calculates the following quantities:
Quantity Description c7beta_minus_trans.value the alpha beta CV METAD...Used to performed metadynamics on one or more collective variables. More detailsARG=enethe input for this action is the scalar output from one or more other actionsPACE=5000the frequency for hill additionBIASFACTOR=60.0use well tempered metadynamics and use this bias factorHEIGHT=2.0the heights of the Gaussian hillsSIGMA=150the widths of the Gaussian hillsGRID_MIN=-500000the lower bounds for the gridGRID_MAX=-100000the upper bounds for the gridFILE=../HILLS_enea file in which the list of added hills is storedLABEL=wtemetad ... METADa label for the action so that its output can be referenced in the input to other actions
The METAD action with label wtemetad calculates the following quantities:
Quantity Description wtemetad.bias the instantaneous value of the bias potential PBMETAD...Used to performed Parallel Bias metadynamics. More detailsARG=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,chi211the input for this action is the scalar output from one or more other actionsSIGMA=0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.1,1,1,1,1,1,1,1,1,1,1,1,1,0.35,0.35,0.35,0.35,0.35,0.35,0.35,0.35,0.35,0.35,0.35,0.35,0.35,0.35,0.35,0.35,0.35,0.35,0.35,0.35,0.35,0.35,0.35,0.35,0.35,0.35,0.35,0.35,0.35,0.35,0.35,0.35,0.35,0.35,0.35,0.35,0.35,0.35,0.35,0.35,0.35,0.35,0.35,0.35,0.35,0.35,0.35,0.35,0.35,0.35,0.35,0.35,0.35,0.35,0.35,0.35,0.35,0.35the widths of the Gaussian hillsHEIGHT=2.5 #kj/molthe height of the Gaussian hills, one for all biasesPACE=1000the frequency for hill addition, one for all biasesBIASFACTOR=140 #max rule baseBF x sqrt(NCV) ~ 100 (BF = ~12 for 10kcal/mol hill height cis/trans isom, CV=131) # TEMP=300use well tempered metadynamics with this bias factor, one for all biasesGRID_MIN=-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,-pithe lower bounds for the gridGRID_MAX=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,pithe upper bounds for the gridLABEL=pba label for the action so that its output can be referenced in the input to other actionsFILE=../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 ... PBMETADfiles in which the lists of added hills are stored, default names are assigned using arguments if FILE is not found
The PBMETAD action with label pb calculates the following quantities:
Quantity Description pb.bias the instantaneous value of the bias potential Print quantities to a file. More detailsARGthe input for this action is the scalar output from one or more other actionsSTRIDE=1000the frequency with which the quantities of interest should be outputFILE=COLVARthe name of the file on which to output these quantities