PLUMED-NEST

Project ID: plumID:24.003
Source: plumed_nest/diff_helices/CH30-+/plumed.dat
Originally used with PLUMED version: 2.8-mod
Stable: zipped raw stdout - zipped raw stderr - stderr
Master: zipped raw stdout - zipped raw stderr - stderr

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

#! vim:ft=plumed
## RESTART

WHOLEMOLECULESThis action is used to rebuild molecules that can become split by the periodic boundary conditions. More details ENTITY0the atoms that make up a molecule that you wish to align=1-826

# CHAIN ONE AND RESIDUE BEFORE LINKER
The WHOLEMOLECULES action with label  calculates somethingCOMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=1-399 LABELa label for the action so that its output can be referenced in the input to other actions=p1
The COM action with label p1 calculates somethingCOMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=1-30 LABELa label for the action so that its output can be referenced in the input to other actions=r1
The COM action with label r1 calculates somethingCOMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=376-399 LABELa label for the action so that its output can be referenced in the input to other actions=r14

# CHAIN TWO AND RESIDUE AFTER LINKER
The COM action with label r14 calculates somethingCOMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=434-826 LABELa label for the action so that its output can be referenced in the input to other actions=p2
The COM action with label p2 calculates somethingCOMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=434-458 LABELa label for the action so that its output can be referenced in the input to other actions=r16
The COM action with label r16 calculates somethingCOMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=804-826 LABELa label for the action so that its output can be referenced in the input to other actions=r30

The COM action with label r30 calculates somethingDISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=p1,p2 LABELa label for the action so that its output can be referenced in the input to other actions=d
The DISTANCE action with label d calculates the following quantities:
 Quantity   
 Description  
d.value
the DISTANCE between this pair of atomsDISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=r14,r16 LABELa label for the action so that its output can be referenced in the input to other actions=in
The DISTANCE action with label in calculates the following quantities:
 Quantity   
 Description  
in.value
the DISTANCE between this pair of atomsDISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=r1,r30 LABELa label for the action so that its output can be referenced in the input to other actions=FRET

The DISTANCE action with label FRET calculates the following quantities:
 Quantity   
 Description  
FRET.value
the DISTANCE between this pair of atomsGYRATIONCalculate the radius of gyration, or other properties related to it. More details TYPE The type of calculation relative to the Gyration Tensor you want to perform=RADIUS ATOMSthe group of atoms that you are calculating the Gyration Tensor for=1,31,64,88,112,145,170,196,225,249,273,296,321,347,376,434,459,492,516,540,573,598,624,653,677,701,724,749,775,804 LABELa label for the action so that its output can be referenced in the input to other actions=rg

The GYRATION action with label rg calculates the following quantities:
 Quantity   
 Description  
rg.value
the radius that was computed from the weightsGYRATIONCalculate the radius of gyration, or other properties related to it. More details TYPE The type of calculation relative to the Gyration Tensor you want to perform=RADIUS ATOMSthe group of atoms that you are calculating the Gyration Tensor for=1,31,64,88,112,145,170,196,225,249,273,296,321,347,376 LABELa label for the action so that its output can be referenced in the input to other actions=rg_1

The GYRATION action with label rg_1 calculates the following quantities:
 Quantity   
 Description  
rg_1.value
the radius that was computed from the weightsGYRATIONCalculate the radius of gyration, or other properties related to it. More details TYPE The type of calculation relative to the Gyration Tensor you want to perform=RADIUS ATOMSthe group of atoms that you are calculating the Gyration Tensor for=434,459,492,516,540,573,598,624,653,677,701,724,749,775,804 LABELa label for the action so that its output can be referenced in the input to other actions=rg_2

# hydrophobic residues 
The GYRATION action with label rg_2 calculates the following quantities:
 Quantity   
 Description  
rg_2.value
the radius that was computed from the weightsCOMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=31-63 LABELa label for the action so that its output can be referenced in the input to other actions=H1
The COM action with label H1 calculates somethingCOMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=112-144 LABELa label for the action so that its output can be referenced in the input to other actions=H2 
The COM action with label H2 calculates somethingCOMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=196-224 LABELa label for the action so that its output can be referenced in the input to other actions=H3
The COM action with label H3 calculates somethingCOMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=273-295 LABELa label for the action so that its output can be referenced in the input to other actions=H4
The COM action with label H4 calculates somethingCOMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=347-375 LABELa label for the action so that its output can be referenced in the input to other actions=H5

The COM action with label H5 calculates somethingCOMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=459-491 LABELa label for the action so that its output can be referenced in the input to other actions=H1_2
The COM action with label H1_2 calculates somethingCOMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=540-572 LABELa label for the action so that its output can be referenced in the input to other actions=H2_2
The COM action with label H2_2 calculates somethingCOMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=624-652 LABELa label for the action so that its output can be referenced in the input to other actions=H3_2
The COM action with label H3_2 calculates somethingCOMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=701-723 LABELa label for the action so that its output can be referenced in the input to other actions=H4_2
The COM action with label H4_2 calculates somethingCOMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=775-803 LABELa label for the action so that its output can be referenced in the input to other actions=H5_2

The COM action with label H5_2 calculates somethingCOORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=H1,H2,H3,H4,H5 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=H1_2,H2_2,H3_2,H4_2,H5_2 R_0The r_0 parameter of the switching function=1.9 NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=2.2 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=100 NN The n parameter of the switching function =20 MM The m parameter of the switching function; 0 implies 2*NN=80 LABELa label for the action so that its output can be referenced in the input to other actions=COORD

The COORDINATION action with label COORD calculates the following quantities:
 Quantity   
 Description  
COORD.value
the value of the coordinationCOORDINATIONCalculate coordination numbers. More details PAIR Pair only 1st element of the 1st group with 1st element in the second, etc GROUPAFirst list of atoms=H1,H2,H3,H4,H5 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=H5_2,H4_2,H3_2,H2_2,H1_2 R_0The r_0 parameter of the switching function=1.9 NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=2.2 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=100 NN The n parameter of the switching function =20 MM The m parameter of the switching function; 0 implies 2*NN=80 LABELa label for the action so that its output can be referenced in the input to other actions=PAIR

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

# dihedrals
# phi: CLP-,N,CA,C

The INCLUDE action with label dihedral.dat calculates somethingphi1: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=29,31,59,62
The TORSION action with label phi1 calculates the following quantities:
 Quantity   
 Description  
phi1.value
the TORSION involving these atomsphi2: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=62,64,83,86
The TORSION action with label phi2 calculates the following quantities:
 Quantity   
 Description  
phi2.value
the TORSION involving these atomsphi3: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=86,88,107,110
The TORSION action with label phi3 calculates the following quantities:
 Quantity   
 Description  
phi3.value
the TORSION involving these atomsphi4: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=110,112,140,143
The TORSION action with label phi4 calculates the following quantities:
 Quantity   
 Description  
phi4.value
the TORSION involving these atomsphi5: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=143,145,165,168
The TORSION action with label phi5 calculates the following quantities:
 Quantity   
 Description  
phi5.value
the TORSION involving these atomsphi6: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=168,170,191,194
The TORSION action with label phi6 calculates the following quantities:
 Quantity   
 Description  
phi6.value
the TORSION involving these atomsphi7: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=194,196,220,223
The TORSION action with label phi7 calculates the following quantities:
 Quantity   
 Description  
phi7.value
the TORSION involving these atomsphi8: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=223,225,244,247
The TORSION action with label phi8 calculates the following quantities:
 Quantity   
 Description  
phi8.value
the TORSION involving these atomsphi9: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=247,249,268,271
The TORSION action with label phi9 calculates the following quantities:
 Quantity   
 Description  
phi9.value
the TORSION involving these atomsphi10: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=271,273,291,294
The TORSION action with label phi10 calculates the following quantities:
 Quantity   
 Description  
phi10.value
the TORSION involving these atomsphi11: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=294,296,316,319
The TORSION action with label phi11 calculates the following quantities:
 Quantity   
 Description  
phi11.value
the TORSION involving these atomsphi12: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=319,321,342,345
The TORSION action with label phi12 calculates the following quantities:
 Quantity   
 Description  
phi12.value
the TORSION involving these atomsphi13: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=345,347,371,374
The TORSION action with label phi13 calculates the following quantities:
 Quantity   
 Description  
phi13.value
the TORSION involving these atomsphi14: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=374,376,395,398

The TORSION action with label phi14 calculates the following quantities:
 Quantity   
 Description  
phi14.value
the TORSION involving these atomsphi17: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=457,459,487,490
The TORSION action with label phi17 calculates the following quantities:
 Quantity   
 Description  
phi17.value
the TORSION involving these atomsphi18: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=490,492,511,514
The TORSION action with label phi18 calculates the following quantities:
 Quantity   
 Description  
phi18.value
the TORSION involving these atomsphi19: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=514,516,535,538
The TORSION action with label phi19 calculates the following quantities:
 Quantity   
 Description  
phi19.value
the TORSION involving these atomsphi20: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=538,540,568,571
The TORSION action with label phi20 calculates the following quantities:
 Quantity   
 Description  
phi20.value
the TORSION involving these atomsphi21: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=571,573,593,596
The TORSION action with label phi21 calculates the following quantities:
 Quantity   
 Description  
phi21.value
the TORSION involving these atomsphi22: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=596,598,619,622
The TORSION action with label phi22 calculates the following quantities:
 Quantity   
 Description  
phi22.value
the TORSION involving these atomsphi23: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=622,624,648,651
The TORSION action with label phi23 calculates the following quantities:
 Quantity   
 Description  
phi23.value
the TORSION involving these atomsphi24: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=651,653,672,675
The TORSION action with label phi24 calculates the following quantities:
 Quantity   
 Description  
phi24.value
the TORSION involving these atomsphi25: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=675,677,696,699
The TORSION action with label phi25 calculates the following quantities:
 Quantity   
 Description  
phi25.value
the TORSION involving these atomsphi26: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=699,701,719,722
The TORSION action with label phi26 calculates the following quantities:
 Quantity   
 Description  
phi26.value
the TORSION involving these atomsphi27: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=722,724,744,747
The TORSION action with label phi27 calculates the following quantities:
 Quantity   
 Description  
phi27.value
the TORSION involving these atomsphi28: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=747,749,770,773
The TORSION action with label phi28 calculates the following quantities:
 Quantity   
 Description  
phi28.value
the TORSION involving these atomsphi29: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=773,775,799,802
The TORSION action with label phi29 calculates the following quantities:
 Quantity   
 Description  
phi29.value
the TORSION involving these atomsphi30: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=802,804,819,822

# psi: NL,CA,CLP,NL+
The TORSION action with label phi30 calculates the following quantities:
 Quantity   
 Description  
phi30.value
the TORSION involving these atomspsi0: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=1,26,29,31
The TORSION action with label psi0 calculates the following quantities:
 Quantity   
 Description  
psi0.value
the TORSION involving these atomspsi1: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=31,59,62,64
The TORSION action with label psi1 calculates the following quantities:
 Quantity   
 Description  
psi1.value
the TORSION involving these atomspsi2: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=64,83,86,88
The TORSION action with label psi2 calculates the following quantities:
 Quantity   
 Description  
psi2.value
the TORSION involving these atomspsi3: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=88,107,110,112
The TORSION action with label psi3 calculates the following quantities:
 Quantity   
 Description  
psi3.value
the TORSION involving these atomspsi4: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=112,140,143,145
The TORSION action with label psi4 calculates the following quantities:
 Quantity   
 Description  
psi4.value
the TORSION involving these atomspsi5: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=145,165,168,170
The TORSION action with label psi5 calculates the following quantities:
 Quantity   
 Description  
psi5.value
the TORSION involving these atomspsi6: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=170,191,194,196
The TORSION action with label psi6 calculates the following quantities:
 Quantity   
 Description  
psi6.value
the TORSION involving these atomspsi7: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=196,220,223,225
The TORSION action with label psi7 calculates the following quantities:
 Quantity   
 Description  
psi7.value
the TORSION involving these atomspsi8: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=225,244,247,249
The TORSION action with label psi8 calculates the following quantities:
 Quantity   
 Description  
psi8.value
the TORSION involving these atomspsi9: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=249,268,271,273
The TORSION action with label psi9 calculates the following quantities:
 Quantity   
 Description  
psi9.value
the TORSION involving these atomspsi10: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=273,291,294,296
The TORSION action with label psi10 calculates the following quantities:
 Quantity   
 Description  
psi10.value
the TORSION involving these atomspsi11: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=296,316,319,321
The TORSION action with label psi11 calculates the following quantities:
 Quantity   
 Description  
psi11.value
the TORSION involving these atomspsi12: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=321,342,345,347
The TORSION action with label psi12 calculates the following quantities:
 Quantity   
 Description  
psi12.value
the TORSION involving these atomspsi13: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=347,371,374,376

The TORSION action with label psi13 calculates the following quantities:
 Quantity   
 Description  
psi13.value
the TORSION involving these atomspsi16: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=434,454,457,459
The TORSION action with label psi16 calculates the following quantities:
 Quantity   
 Description  
psi16.value
the TORSION involving these atomspsi17: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=459,487,490,492
The TORSION action with label psi17 calculates the following quantities:
 Quantity   
 Description  
psi17.value
the TORSION involving these atomspsi18: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=492,511,514,516
The TORSION action with label psi18 calculates the following quantities:
 Quantity   
 Description  
psi18.value
the TORSION involving these atomspsi19: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=516,535,538,540
The TORSION action with label psi19 calculates the following quantities:
 Quantity   
 Description  
psi19.value
the TORSION involving these atomspsi20: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=540,568,571,573
The TORSION action with label psi20 calculates the following quantities:
 Quantity   
 Description  
psi20.value
the TORSION involving these atomspsi21: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=573,593,596,598
The TORSION action with label psi21 calculates the following quantities:
 Quantity   
 Description  
psi21.value
the TORSION involving these atomspsi22: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=598,619,622,624
The TORSION action with label psi22 calculates the following quantities:
 Quantity   
 Description  
psi22.value
the TORSION involving these atomspsi23: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=624,648,651,653
The TORSION action with label psi23 calculates the following quantities:
 Quantity   
 Description  
psi23.value
the TORSION involving these atomspsi24: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=653,672,675,677
The TORSION action with label psi24 calculates the following quantities:
 Quantity   
 Description  
psi24.value
the TORSION involving these atomspsi25: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=677,696,699,701
The TORSION action with label psi25 calculates the following quantities:
 Quantity   
 Description  
psi25.value
the TORSION involving these atomspsi26: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=701,719,722,724
The TORSION action with label psi26 calculates the following quantities:
 Quantity   
 Description  
psi26.value
the TORSION involving these atomspsi27: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=724,744,747,749
The TORSION action with label psi27 calculates the following quantities:
 Quantity   
 Description  
psi27.value
the TORSION involving these atomspsi28: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=749,770,773,775
The TORSION action with label psi28 calculates the following quantities:
 Quantity   
 Description  
psi28.value
the TORSION involving these atomspsi29: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=775,799,802,804

# omega: CA-, C-, N, CA

The TORSION action with label psi29 calculates the following quantities:
 Quantity   
 Description  
psi29.value
the TORSION involving these atomsomega1: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=26,29,31,59
The TORSION action with label omega1 calculates the following quantities:
 Quantity   
 Description  
omega1.value
the TORSION involving these atomsomega2: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=59,62,64,83
The TORSION action with label omega2 calculates the following quantities:
 Quantity   
 Description  
omega2.value
the TORSION involving these atomsomega3: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=83,86,88,107
The TORSION action with label omega3 calculates the following quantities:
 Quantity   
 Description  
omega3.value
the TORSION involving these atomsomega4: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=107,110,112,140
The TORSION action with label omega4 calculates the following quantities:
 Quantity   
 Description  
omega4.value
the TORSION involving these atomsomega5: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=140,143,145,165
The TORSION action with label omega5 calculates the following quantities:
 Quantity   
 Description  
omega5.value
the TORSION involving these atomsomega6: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=165,168,170,191
The TORSION action with label omega6 calculates the following quantities:
 Quantity   
 Description  
omega6.value
the TORSION involving these atomsomega7: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=191,194,196,220
The TORSION action with label omega7 calculates the following quantities:
 Quantity   
 Description  
omega7.value
the TORSION involving these atomsomega8: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=220,223,225,244
The TORSION action with label omega8 calculates the following quantities:
 Quantity   
 Description  
omega8.value
the TORSION involving these atomsomega9: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=244,247,249,268
The TORSION action with label omega9 calculates the following quantities:
 Quantity   
 Description  
omega9.value
the TORSION involving these atomsomega10: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=268,271,273,291
The TORSION action with label omega10 calculates the following quantities:
 Quantity   
 Description  
omega10.value
the TORSION involving these atomsomega11: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=291,294,296,316
The TORSION action with label omega11 calculates the following quantities:
 Quantity   
 Description  
omega11.value
the TORSION involving these atomsomega12: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=316,319,321,342
The TORSION action with label omega12 calculates the following quantities:
 Quantity   
 Description  
omega12.value
the TORSION involving these atomsomega13: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=342,345,347,371
The TORSION action with label omega13 calculates the following quantities:
 Quantity   
 Description  
omega13.value
the TORSION involving these atomsomega14: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=371,374,376,395

The TORSION action with label omega14 calculates the following quantities:
 Quantity   
 Description  
omega14.value
the TORSION involving these atomsomega17: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=454,457,459,487
The TORSION action with label omega17 calculates the following quantities:
 Quantity   
 Description  
omega17.value
the TORSION involving these atomsomega18: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=487,490,492,511
The TORSION action with label omega18 calculates the following quantities:
 Quantity   
 Description  
omega18.value
the TORSION involving these atomsomega19: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=511,514,516,535
The TORSION action with label omega19 calculates the following quantities:
 Quantity   
 Description  
omega19.value
the TORSION involving these atomsomega20: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=535,538,540,568
The TORSION action with label omega20 calculates the following quantities:
 Quantity   
 Description  
omega20.value
the TORSION involving these atomsomega21: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=568,571,573,593
The TORSION action with label omega21 calculates the following quantities:
 Quantity   
 Description  
omega21.value
the TORSION involving these atomsomega22: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=593,596,598,619
The TORSION action with label omega22 calculates the following quantities:
 Quantity   
 Description  
omega22.value
the TORSION involving these atomsomega23: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=619,622,624,648
The TORSION action with label omega23 calculates the following quantities:
 Quantity   
 Description  
omega23.value
the TORSION involving these atomsomega24: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=648,651,653,672
The TORSION action with label omega24 calculates the following quantities:
 Quantity   
 Description  
omega24.value
the TORSION involving these atomsomega25: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=672,675,677,696
The TORSION action with label omega25 calculates the following quantities:
 Quantity   
 Description  
omega25.value
the TORSION involving these atomsomega26: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=696,699,701,719
The TORSION action with label omega26 calculates the following quantities:
 Quantity   
 Description  
omega26.value
the TORSION involving these atomsomega27: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=719,722,724,744
The TORSION action with label omega27 calculates the following quantities:
 Quantity   
 Description  
omega27.value
the TORSION involving these atomsomega28: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=744,747,749,770
The TORSION action with label omega28 calculates the following quantities:
 Quantity   
 Description  
omega28.value
the TORSION involving these atomsomega29: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=770,773,775,799
The TORSION action with label omega29 calculates the following quantities:
 Quantity   
 Description  
omega29.value
the TORSION involving these atomsomega30: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=799,802,804,819

# chi 1 dihedral: CA, NL, CB1, CG (or other)

The TORSION action with label omega30 calculates the following quantities:
 Quantity   
 Description  
omega30.value
the TORSION involving these atomschi1: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=59,31,32,35
The TORSION action with label chi1 calculates the following quantities:
 Quantity   
 Description  
chi1.value
the TORSION involving these atomschi2: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=83,64,65,71
The TORSION action with label chi2 calculates the following quantities:
 Quantity   
 Description  
chi2.value
the TORSION involving these atomschi3: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=107,88,89,95
The TORSION action with label chi3 calculates the following quantities:
 Quantity   
 Description  
chi3.value
the TORSION involving these atomschi4: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=140,112,113,116
The TORSION action with label chi4 calculates the following quantities:
 Quantity   
 Description  
chi4.value
the TORSION involving these atomschi5: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=165,145,146,152
The TORSION action with label chi5 calculates the following quantities:
 Quantity   
 Description  
chi5.value
the TORSION involving these atomschi6: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=191,170,171,177
The TORSION action with label chi6 calculates the following quantities:
 Quantity   
 Description  
chi6.value
the TORSION involving these atomschi7: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=220,196,197,203
The TORSION action with label chi7 calculates the following quantities:
 Quantity   
 Description  
chi7.value
the TORSION involving these atomschi8: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=244,225,226,232
The TORSION action with label chi8 calculates the following quantities:
 Quantity   
 Description  
chi8.value
the TORSION involving these atomschi9: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=268,249,250,256
The TORSION action with label chi9 calculates the following quantities:
 Quantity   
 Description  
chi9.value
the TORSION involving these atomschi10: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=291,273,274,280
The TORSION action with label chi10 calculates the following quantities:
 Quantity   
 Description  
chi10.value
the TORSION involving these atomschi11: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=316,296,297,303
The TORSION action with label chi11 calculates the following quantities:
 Quantity   
 Description  
chi11.value
the TORSION involving these atomschi12: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=342,321,322,328
The TORSION action with label chi12 calculates the following quantities:
 Quantity   
 Description  
chi12.value
the TORSION involving these atomschi13: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=371,347,348,354
The TORSION action with label chi13 calculates the following quantities:
 Quantity   
 Description  
chi13.value
the TORSION involving these atomschi14: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=395,376,377,383

The TORSION action with label chi14 calculates the following quantities:
 Quantity   
 Description  
chi14.value
the TORSION involving these atomschi16: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=454,434,435,441
The TORSION action with label chi16 calculates the following quantities:
 Quantity   
 Description  
chi16.value
the TORSION involving these atomschi17: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=487,459,460,463
The TORSION action with label chi17 calculates the following quantities:
 Quantity   
 Description  
chi17.value
the TORSION involving these atomschi18: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=511,492,493,499
The TORSION action with label chi18 calculates the following quantities:
 Quantity   
 Description  
chi18.value
the TORSION involving these atomschi19: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=535,516,517,523
The TORSION action with label chi19 calculates the following quantities:
 Quantity   
 Description  
chi19.value
the TORSION involving these atomschi20: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=568,540,541,544
The TORSION action with label chi20 calculates the following quantities:
 Quantity   
 Description  
chi20.value
the TORSION involving these atomschi21: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=593,573,574,580
The TORSION action with label chi21 calculates the following quantities:
 Quantity   
 Description  
chi21.value
the TORSION involving these atomschi22: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=619,598,599,605
The TORSION action with label chi22 calculates the following quantities:
 Quantity   
 Description  
chi22.value
the TORSION involving these atomschi23: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=648,624,625,631
The TORSION action with label chi23 calculates the following quantities:
 Quantity   
 Description  
chi23.value
the TORSION involving these atomschi24: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=672,653,654,660
The TORSION action with label chi24 calculates the following quantities:
 Quantity   
 Description  
chi24.value
the TORSION involving these atomschi25: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=696,677,678,684
The TORSION action with label chi25 calculates the following quantities:
 Quantity   
 Description  
chi25.value
the TORSION involving these atomschi26: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=719,701,702,708
The TORSION action with label chi26 calculates the following quantities:
 Quantity   
 Description  
chi26.value
the TORSION involving these atomschi27: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=744,724,725,731
The TORSION action with label chi27 calculates the following quantities:
 Quantity   
 Description  
chi27.value
the TORSION involving these atomschi28: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=770,749,750,756
The TORSION action with label chi28 calculates the following quantities:
 Quantity   
 Description  
chi28.value
the TORSION involving these atomschi29: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=799,775,776,782

# chi 2 dihedral: NL,CB1,CG,CD1
The TORSION action with label chi29 calculates the following quantities:
 Quantity   
 Description  
chi29.value
the TORSION involving these atomschia: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=31,32,35,37
The TORSION action with label chia calculates the following quantities:
 Quantity   
 Description  
chia.value
the TORSION involving these atomschib: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=112,113,116,118
The TORSION action with label chib calculates the following quantities:
 Quantity   
 Description  
chib.value
the TORSION involving these atomschic: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=196,197,203,205
The TORSION action with label chic calculates the following quantities:
 Quantity   
 Description  
chic.value
the TORSION involving these atomschid: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=273,274,280,281
The TORSION action with label chid calculates the following quantities:
 Quantity   
 Description  
chid.value
the TORSION involving these atomschie: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=347,348,354,356

The TORSION action with label chie calculates the following quantities:
 Quantity   
 Description  
chie.value
the TORSION involving these atomschif: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=459,460,463,465
The TORSION action with label chif calculates the following quantities:
 Quantity   
 Description  
chif.value
the TORSION involving these atomschig: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=540,541,544,546
The TORSION action with label chig calculates the following quantities:
 Quantity   
 Description  
chig.value
the TORSION involving these atomschih: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=624,625,631,633
The TORSION action with label chih calculates the following quantities:
 Quantity   
 Description  
chih.value
the TORSION involving these atomschii: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=701,702,708,709
The TORSION action with label chii calculates the following quantities:
 Quantity   
 Description  
chii.value
the TORSION involving these atomschij: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=775,776,782,784

# chi 3 dihedral: CB1, CG, CC, CD1 just for NDPEs
The TORSION action with label chij calculates the following quantities:
 Quantity   
 Description  
chij.value
the TORSION involving these atomschiaa: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=32,35,37,38
The TORSION action with label chiaa calculates the following quantities:
 Quantity   
 Description  
chiaa.value
the TORSION involving these atomschiba: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=113,116,118,119
The TORSION action with label chiba calculates the following quantities:
 Quantity   
 Description  
chiba.value
the TORSION involving these atomschifa: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=460,463,465,466
The TORSION action with label chifa calculates the following quantities:
 Quantity   
 Description  
chifa.value
the TORSION involving these atomschiga: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=541,544,546,547
# --- End of included input --- The TORSION action with label chiga calculates the following quantities:
 Quantity   
 Description  
chiga.value
the TORSION involving these atomsINCLUDEIncludes an external input file, similar to #include in C preprocessor. More details. Show included file FILEfile to be included=alphabeta.dat
# The command:
# INCLUDE FILE=alphabeta.dat
# ensures PLUMED loads the contents of the file called alphabeta.dat
# The contents of this file are shown below (click the red comment to hide them).
#! vim:ft=plumed

# updated dihedrals 1/12/23
# phi: CLP-,NL,CA,CLP
# positive 1.57 is alpha d plus, negative is alpha d minus
The INCLUDE action with label alphabeta.dat calculates somethingALPHABETAMeasures a distance including pbc between the instantaneous values of a set of torsional angles and set of reference values. More details ...
ATOMS1the atoms involved for each of the torsions you wish to calculate=29,31,59,62 REFERENCE1the reference values for each of the torsional angles=-1.40
ATOMS2the atoms involved for each of the torsions you wish to calculate=62,64,83,86 REFERENCE2the reference values for each of the torsional angles=-1.40 
ATOMS3the atoms involved for each of the torsions you wish to calculate=86,88,107,110 REFERENCE3the reference values for each of the torsional angles=-1.40 
ATOMS4the atoms involved for each of the torsions you wish to calculate=110,112,140,143 REFERENCE4the reference values for each of the torsional angles=-1.40 
ATOMS5the atoms involved for each of the torsions you wish to calculate=143,145,165,168 REFERENCE5the reference values for each of the torsional angles=-1.40 
ATOMS6the atoms involved for each of the torsions you wish to calculate=168,170,191,194 REFERENCE6the reference values for each of the torsional angles=-1.40 
ATOMS7the atoms involved for each of the torsions you wish to calculate=194,196,220,223 REFERENCE7the reference values for each of the torsional angles=-1.40 
ATOMS8the atoms involved for each of the torsions you wish to calculate=223,225,244,247 REFERENCE8the reference values for each of the torsional angles=-1.40 
ATOMS9the atoms involved for each of the torsions you wish to calculate=247,249,268,271 REFERENCE9the reference values for each of the torsional angles=-1.40 
ATOMS10the atoms involved for each of the torsions you wish to calculate=271,273,291,294 REFERENCE10the reference values for each of the torsional angles=-1.40
ATOMS11the atoms involved for each of the torsions you wish to calculate=294,296,316,319 REFERENCE11the reference values for each of the torsional angles=-1.40
ATOMS12the atoms involved for each of the torsions you wish to calculate=319,321,342,345 REFERENCE12the reference values for each of the torsional angles=-1.40
ATOMS13the atoms involved for each of the torsions you wish to calculate=345,347,371,374 REFERENCE13the reference values for each of the torsional angles=-1.40
ATOMS14the atoms involved for each of the torsions you wish to calculate=374,376,395,398 REFERENCE14the reference values for each of the torsional angles=-1.40
LABELa label for the action so that its output can be referenced in the input to other actions=AB_PHI0
... ALPHABETA

The ALPHABETA action with label AB_PHI0 calculates the following quantities:
 Quantity   
 Description  
AB_PHI0.value
the alpha beta CVALPHABETAMeasures a distance including pbc between the instantaneous values of a set of torsional angles and set of reference values. More details ...
ATOMS1the atoms involved for each of the torsions you wish to calculate=457,459,487,490 REFERENCE1the reference values for each of the torsional angles=1.40
ATOMS2the atoms involved for each of the torsions you wish to calculate=490,492,511,514 REFERENCE2the reference values for each of the torsional angles=1.40
ATOMS3the atoms involved for each of the torsions you wish to calculate=514,516,535,538 REFERENCE3the reference values for each of the torsional angles=1.40
ATOMS4the atoms involved for each of the torsions you wish to calculate=538,540,568,571 REFERENCE4the reference values for each of the torsional angles=1.40
ATOMS5the atoms involved for each of the torsions you wish to calculate=571,573,593,596 REFERENCE5the reference values for each of the torsional angles=1.40
ATOMS6the atoms involved for each of the torsions you wish to calculate=596,598,619,622 REFERENCE6the reference values for each of the torsional angles=1.40
ATOMS7the atoms involved for each of the torsions you wish to calculate=622,624,648,651 REFERENCE7the reference values for each of the torsional angles=1.40
ATOMS8the atoms involved for each of the torsions you wish to calculate=651,653,672,675 REFERENCE8the reference values for each of the torsional angles=1.40
ATOMS9the atoms involved for each of the torsions you wish to calculate=675,677,696,699 REFERENCE9the reference values for each of the torsional angles=1.40
ATOMS10the atoms involved for each of the torsions you wish to calculate=699,701,719,722 REFERENCE10the reference values for each of the torsional angles=1.40
ATOMS11the atoms involved for each of the torsions you wish to calculate=722,724,744,747 REFERENCE11the reference values for each of the torsional angles=1.40
ATOMS12the atoms involved for each of the torsions you wish to calculate=747,749,770,773 REFERENCE12the reference values for each of the torsional angles=1.40
ATOMS13the atoms involved for each of the torsions you wish to calculate=773,775,799,802 REFERENCE13the reference values for each of the torsional angles=1.40
ATOMS14the atoms involved for each of the torsions you wish to calculate=802,804,819,822 REFERENCE14the reference values for each of the torsional angles=1.40
LABELa label for the action so that its output can be referenced in the input to other actions=AB_PHI1
... ALPHABETA

# psi: NL,CA,CLP,NL+

The ALPHABETA action with label AB_PHI1 calculates the following quantities:
 Quantity   
 Description  
AB_PHI1.value
the alpha beta CVALPHABETAMeasures a distance including pbc between the instantaneous values of a set of torsional angles and set of reference values. More details ...
ATOMS1the atoms involved for each of the torsions you wish to calculate=1,26,29,31 REFERENCE1the reference values for each of the torsional angles=2.97
ATOMS2the atoms involved for each of the torsions you wish to calculate=31,59,62,64 REFERENCE2the reference values for each of the torsional angles=2.97
ATOMS3the atoms involved for each of the torsions you wish to calculate=64,83,86,88 REFERENCE3the reference values for each of the torsional angles=2.97
ATOMS4the atoms involved for each of the torsions you wish to calculate=88,107,110,112 REFERENCE4the reference values for each of the torsional angles=2.97
ATOMS5the atoms involved for each of the torsions you wish to calculate=112,140,143,145 REFERENCE5the reference values for each of the torsional angles=2.97
ATOMS6the atoms involved for each of the torsions you wish to calculate=145,165,168,170 REFERENCE6the reference values for each of the torsional angles=2.97
ATOMS7the atoms involved for each of the torsions you wish to calculate=170,191,194,196 REFERENCE7the reference values for each of the torsional angles=2.97
ATOMS8the atoms involved for each of the torsions you wish to calculate=196,220,223,225 REFERENCE8the reference values for each of the torsional angles=2.97
ATOMS9the atoms involved for each of the torsions you wish to calculate=225,244,247,249 REFERENCE9the reference values for each of the torsional angles=2.97
ATOMS10the atoms involved for each of the torsions you wish to calculate=249,268,271,273 REFERENCE10the reference values for each of the torsional angles=2.97
ATOMS11the atoms involved for each of the torsions you wish to calculate=273,291,294,296 REFERENCE11the reference values for each of the torsional angles=2.97
ATOMS12the atoms involved for each of the torsions you wish to calculate=296,316,319,321 REFERENCE12the reference values for each of the torsional angles=2.97
ATOMS13the atoms involved for each of the torsions you wish to calculate=321,342,345,347 REFERENCE13the reference values for each of the torsional angles=2.97
ATOMS14the atoms involved for each of the torsions you wish to calculate=347,371,374,376 REFERENCE14the reference values for each of the torsional angles=2.97
LABELa label for the action so that its output can be referenced in the input to other actions=AB_PSI0
... ALPHABETA

The ALPHABETA action with label AB_PSI0 calculates the following quantities:
 Quantity   
 Description  
AB_PSI0.value
the alpha beta CVALPHABETAMeasures a distance including pbc between the instantaneous values of a set of torsional angles and set of reference values. More details ...
ATOMS1the atoms involved for each of the torsions you wish to calculate=434,454,457,459 REFERENCE1the reference values for each of the torsional angles=2.97
ATOMS2the atoms involved for each of the torsions you wish to calculate=459,487,490,492 REFERENCE2the reference values for each of the torsional angles=2.97
ATOMS3the atoms involved for each of the torsions you wish to calculate=492,511,514,516 REFERENCE3the reference values for each of the torsional angles=2.97
ATOMS4the atoms involved for each of the torsions you wish to calculate=516,535,538,540 REFERENCE4the reference values for each of the torsional angles=2.97
ATOMS5the atoms involved for each of the torsions you wish to calculate=540,568,571,573 REFERENCE5the reference values for each of the torsional angles=2.97
ATOMS6the atoms involved for each of the torsions you wish to calculate=573,593,596,598 REFERENCE6the reference values for each of the torsional angles=2.97
ATOMS7the atoms involved for each of the torsions you wish to calculate=598,619,622,624 REFERENCE7the reference values for each of the torsional angles=2.97
ATOMS8the atoms involved for each of the torsions you wish to calculate=624,648,651,653 REFERENCE8the reference values for each of the torsional angles=2.97
ATOMS9the atoms involved for each of the torsions you wish to calculate=653,672,675,677 REFERENCE9the reference values for each of the torsional angles=2.97
ATOMS10the atoms involved for each of the torsions you wish to calculate=677,696,699,701 REFERENCE10the reference values for each of the torsional angles=2.97
ATOMS11the atoms involved for each of the torsions you wish to calculate=701,719,722,724 REFERENCE11the reference values for each of the torsional angles=2.97  
ATOMS12the atoms involved for each of the torsions you wish to calculate=724,744,747,749 REFERENCE12the reference values for each of the torsional angles=2.97
ATOMS13the atoms involved for each of the torsions you wish to calculate=749,770,773,775 REFERENCE13the reference values for each of the torsional angles=2.97
ATOMS14the atoms involved for each of the torsions you wish to calculate=775,799,802,804 REFERENCE14the reference values for each of the torsional angles=2.97
LABELa label for the action so that its output can be referenced in the input to other actions=AB_PSI1
... ALPHABETA

# omega: CA-, C-, N, CA
The ALPHABETA action with label AB_PSI1 calculates the following quantities:
 Quantity   
 Description  
AB_PSI1.value
the alpha beta CVALPHABETAMeasures a distance including pbc between the instantaneous values of a set of torsional angles and set of reference values. More details ...
ATOMS1the atoms involved for each of the torsions you wish to calculate=26,29,31,59 REFERENCE1the reference values for each of the torsional angles=0    
ATOMS2the atoms involved for each of the torsions you wish to calculate=59,62,64,83 REFERENCE2the reference values for each of the torsional angles=0
ATOMS3the atoms involved for each of the torsions you wish to calculate=83,86,88,107 REFERENCE3the reference values for each of the torsional angles=0
ATOMS4the atoms involved for each of the torsions you wish to calculate=107,110,112,140 REFERENCE4the reference values for each of the torsional angles=0
ATOMS5the atoms involved for each of the torsions you wish to calculate=140,143,145,165 REFERENCE5the reference values for each of the torsional angles=0
ATOMS6the atoms involved for each of the torsions you wish to calculate=165,168,170,191 REFERENCE6the reference values for each of the torsional angles=0
ATOMS7the atoms involved for each of the torsions you wish to calculate=191,194,196,220 REFERENCE7the reference values for each of the torsional angles=0
ATOMS8the atoms involved for each of the torsions you wish to calculate=220,223,225,244 REFERENCE8the reference values for each of the torsional angles=0
ATOMS9the atoms involved for each of the torsions you wish to calculate=244,247,249,268 REFERENCE9the reference values for each of the torsional angles=0
ATOMS10the atoms involved for each of the torsions you wish to calculate=268,271,273,291 REFERENCE10the reference values for each of the torsional angles=0
ATOMS11the atoms involved for each of the torsions you wish to calculate=291,294,296,316 REFERENCE11the reference values for each of the torsional angles=0
ATOMS12the atoms involved for each of the torsions you wish to calculate=316,319,321,342 REFERENCE12the reference values for each of the torsional angles=0
ATOMS13the atoms involved for each of the torsions you wish to calculate=342,345,347,371 REFERENCE13the reference values for each of the torsional angles=0
ATOMS14the atoms involved for each of the torsions you wish to calculate=371,374,376,395 REFERENCE14the reference values for each of the torsional angles=0
LABELa label for the action so that its output can be referenced in the input to other actions=AB_O0
... ALPHABETA

The ALPHABETA action with label AB_O0 calculates the following quantities:
 Quantity   
 Description  
AB_O0.value
the alpha beta CVALPHABETAMeasures a distance including pbc between the instantaneous values of a set of torsional angles and set of reference values. More details ...
ATOMS1the atoms involved for each of the torsions you wish to calculate=454,457,459,487 REFERENCE1the reference values for each of the torsional angles=0    
ATOMS2the atoms involved for each of the torsions you wish to calculate=487,490,492,511 REFERENCE2the reference values for each of the torsional angles=0
ATOMS3the atoms involved for each of the torsions you wish to calculate=511,514,516,535 REFERENCE3the reference values for each of the torsional angles=0
ATOMS4the atoms involved for each of the torsions you wish to calculate=535,538,540,568 REFERENCE4the reference values for each of the torsional angles=0
ATOMS5the atoms involved for each of the torsions you wish to calculate=568,571,573,593 REFERENCE5the reference values for each of the torsional angles=0
ATOMS6the atoms involved for each of the torsions you wish to calculate=593,596,598,619 REFERENCE6the reference values for each of the torsional angles=0
ATOMS7the atoms involved for each of the torsions you wish to calculate=619,622,624,648 REFERENCE7the reference values for each of the torsional angles=0
ATOMS8the atoms involved for each of the torsions you wish to calculate=648,651,653,672 REFERENCE8the reference values for each of the torsional angles=0
ATOMS9the atoms involved for each of the torsions you wish to calculate=672,675,677,696 REFERENCE9the reference values for each of the torsional angles=0
ATOMS10the atoms involved for each of the torsions you wish to calculate=696,699,701,719 REFERENCE10the reference values for each of the torsional angles=0
ATOMS11the atoms involved for each of the torsions you wish to calculate=719,722,724,744 REFERENCE11the reference values for each of the torsional angles=0
ATOMS12the atoms involved for each of the torsions you wish to calculate=744,747,749,770 REFERENCE12the reference values for each of the torsional angles=0
ATOMS13the atoms involved for each of the torsions you wish to calculate=770,773,775,799 REFERENCE13the reference values for each of the torsional angles=0
ATOMS14the atoms involved for each of the torsions you wish to calculate=799,802,804,819 REFERENCE14the reference values for each of the torsional angles=0
LABELa label for the action so that its output can be referenced in the input to other actions=AB_O1
... ALPHABETA

# --- End of included input --- The ALPHABETA action with label AB_O1 calculates the following quantities:
 Quantity   
 Description  
AB_O1.value
the alpha beta CVINCLUDEIncludes an external input file, similar to #include in C preprocessor. More details. Show included file FILEfile to be included=minima.dat
# The command:
# INCLUDE FILE=minima.dat
# ensures PLUMED loads the contents of the file called minima.dat
# The contents of this file are shown below (click the red comment to hide them).
#! vim:ft=plumed

# phi = positive 1.57 is alpha d plus, negative is alpha d minus
# psi = 3.14, omega = 0

# first helix
The INCLUDE action with label minima.dat calculates somethingALPHABETAMeasures a distance including pbc between the instantaneous values of a set of torsional angles and set of reference values. More details ...
ATOMS1the atoms involved for each of the torsions you wish to calculate=29,31,59,62 REFERENCE1the reference values for each of the torsional angles=-1.40
ATOMS2the atoms involved for each of the torsions you wish to calculate=62,64,83,86 REFERENCE2the reference values for each of the torsional angles=-1.40
ATOMS3the atoms involved for each of the torsions you wish to calculate=86,88,107,110 REFERENCE3the reference values for each of the torsional angles=-1.40
ATOMS4the atoms involved for each of the torsions you wish to calculate=110,112,140,143 REFERENCE4the reference values for each of the torsional angles=-1.40
ATOMS5the atoms involved for each of the torsions you wish to calculate=143,145,165,168 REFERENCE5the reference values for each of the torsional angles=-1.40
ATOMS6the atoms involved for each of the torsions you wish to calculate=168,170,191,194 REFERENCE6the reference values for each of the torsional angles=-1.40
ATOMS7the atoms involved for each of the torsions you wish to calculate=194,196,220,223 REFERENCE7the reference values for each of the torsional angles=-1.40
ATOMS8the atoms involved for each of the torsions you wish to calculate=223,225,244,247 REFERENCE8the reference values for each of the torsional angles=-1.40
ATOMS9the atoms involved for each of the torsions you wish to calculate=247,249,268,271 REFERENCE9the reference values for each of the torsional angles=-1.40
ATOMS10the atoms involved for each of the torsions you wish to calculate=271,273,291,294 REFERENCE10the reference values for each of the torsional angles=-1.40
ATOMS11the atoms involved for each of the torsions you wish to calculate=294,296,316,319 REFERENCE11the reference values for each of the torsional angles=-1.40
ATOMS12the atoms involved for each of the torsions you wish to calculate=319,321,342,345 REFERENCE12the reference values for each of the torsional angles=-1.40
ATOMS13the atoms involved for each of the torsions you wish to calculate=345,347,371,374 REFERENCE13the reference values for each of the torsional angles=-1.40
ATOMS14the atoms involved for each of the torsions you wish to calculate=374,376,395,398 REFERENCE14the reference values for each of the torsional angles=-1.40
ATOMS15the atoms involved for each of the torsions you wish to calculate=1,26,29,31 REFERENCE15the reference values for each of the torsional angles=2.97
ATOMS16the atoms involved for each of the torsions you wish to calculate=31,59,62,64 REFERENCE16the reference values for each of the torsional angles=2.97
ATOMS17the atoms involved for each of the torsions you wish to calculate=64,83,86,88 REFERENCE17the reference values for each of the torsional angles=2.97
ATOMS18the atoms involved for each of the torsions you wish to calculate=88,107,110,112 REFERENCE18the reference values for each of the torsional angles=2.97
ATOMS19the atoms involved for each of the torsions you wish to calculate=112,140,143,145 REFERENCE19the reference values for each of the torsional angles=2.97
ATOMS20the atoms involved for each of the torsions you wish to calculate=145,165,168,170 REFERENCE20the reference values for each of the torsional angles=2.97
ATOMS21the atoms involved for each of the torsions you wish to calculate=170,191,194,196 REFERENCE21the reference values for each of the torsional angles=2.97
ATOMS22the atoms involved for each of the torsions you wish to calculate=196,220,223,225 REFERENCE22the reference values for each of the torsional angles=2.97
ATOMS23the atoms involved for each of the torsions you wish to calculate=225,244,247,249 REFERENCE23the reference values for each of the torsional angles=2.97
ATOMS24the atoms involved for each of the torsions you wish to calculate=249,268,271,273 REFERENCE24the reference values for each of the torsional angles=2.97
ATOMS25the atoms involved for each of the torsions you wish to calculate=273,291,294,296 REFERENCE25the reference values for each of the torsional angles=2.97
ATOMS26the atoms involved for each of the torsions you wish to calculate=296,316,319,321 REFERENCE26the reference values for each of the torsional angles=2.97
ATOMS27the atoms involved for each of the torsions you wish to calculate=321,342,345,347 REFERENCE27the reference values for each of the torsional angles=2.97
ATOMS28the atoms involved for each of the torsions you wish to calculate=347,371,374,376 REFERENCE28the reference values for each of the torsional angles=2.97
ATOMS29the atoms involved for each of the torsions you wish to calculate=26,29,31,59 REFERENCE29the reference values for each of the torsional angles=0
ATOMS30the atoms involved for each of the torsions you wish to calculate=59,62,64,83 REFERENCE30the reference values for each of the torsional angles=0
ATOMS31the atoms involved for each of the torsions you wish to calculate=83,86,88,107 REFERENCE31the reference values for each of the torsional angles=0
ATOMS32the atoms involved for each of the torsions you wish to calculate=107,110,112,140 REFERENCE32the reference values for each of the torsional angles=0
ATOMS33the atoms involved for each of the torsions you wish to calculate=140,143,145,165 REFERENCE33the reference values for each of the torsional angles=0
ATOMS34the atoms involved for each of the torsions you wish to calculate=165,168,170,191 REFERENCE34the reference values for each of the torsional angles=0
ATOMS35the atoms involved for each of the torsions you wish to calculate=191,194,196,220 REFERENCE35the reference values for each of the torsional angles=0
ATOMS36the atoms involved for each of the torsions you wish to calculate=220,223,225,244 REFERENCE36the reference values for each of the torsional angles=0
ATOMS37the atoms involved for each of the torsions you wish to calculate=244,247,249,268 REFERENCE37the reference values for each of the torsional angles=0
ATOMS38the atoms involved for each of the torsions you wish to calculate=268,271,273,291 REFERENCE38the reference values for each of the torsional angles=0
ATOMS39the atoms involved for each of the torsions you wish to calculate=291,294,296,316 REFERENCE39the reference values for each of the torsional angles=0
ATOMS40the atoms involved for each of the torsions you wish to calculate=316,319,321,342 REFERENCE40the reference values for each of the torsional angles=0
ATOMS41the atoms involved for each of the torsions you wish to calculate=342,345,347,371 REFERENCE41the reference values for each of the torsional angles=0
ATOMS42the atoms involved for each of the torsions you wish to calculate=371,374,376,395 REFERENCE42the reference values for each of the torsional angles=0
LABELa label for the action so that its output can be referenced in the input to other actions=AB_1
... ALPHABETA

#second helix
The ALPHABETA action with label AB_1 calculates the following quantities:
 Quantity   
 Description  
AB_1.value
the alpha beta CVALPHABETAMeasures a distance including pbc between the instantaneous values of a set of torsional angles and set of reference values. More details ...
ATOMS1the atoms involved for each of the torsions you wish to calculate=457,459,487,490 REFERENCE1the reference values for each of the torsional angles=1.40
ATOMS2the atoms involved for each of the torsions you wish to calculate=490,492,511,514 REFERENCE2the reference values for each of the torsional angles=1.40
ATOMS3the atoms involved for each of the torsions you wish to calculate=514,516,535,538 REFERENCE3the reference values for each of the torsional angles=1.40
ATOMS4the atoms involved for each of the torsions you wish to calculate=538,540,568,571 REFERENCE4the reference values for each of the torsional angles=1.40
ATOMS5the atoms involved for each of the torsions you wish to calculate=571,573,593,596 REFERENCE5the reference values for each of the torsional angles=1.40
ATOMS6the atoms involved for each of the torsions you wish to calculate=596,598,619,622 REFERENCE6the reference values for each of the torsional angles=1.40
ATOMS7the atoms involved for each of the torsions you wish to calculate=622,624,648,651 REFERENCE7the reference values for each of the torsional angles=1.40
ATOMS8the atoms involved for each of the torsions you wish to calculate=651,653,672,675 REFERENCE8the reference values for each of the torsional angles=1.40
ATOMS9the atoms involved for each of the torsions you wish to calculate=675,677,696,699 REFERENCE9the reference values for each of the torsional angles=1.40
ATOMS10the atoms involved for each of the torsions you wish to calculate=699,701,719,722 REFERENCE10the reference values for each of the torsional angles=1.40
ATOMS11the atoms involved for each of the torsions you wish to calculate=722,724,744,747 REFERENCE11the reference values for each of the torsional angles=1.40
ATOMS12the atoms involved for each of the torsions you wish to calculate=747,749,770,773 REFERENCE12the reference values for each of the torsional angles=1.40
ATOMS13the atoms involved for each of the torsions you wish to calculate=773,775,799,802 REFERENCE13the reference values for each of the torsional angles=1.40
ATOMS14the atoms involved for each of the torsions you wish to calculate=802,804,819,822 REFERENCE14the reference values for each of the torsional angles=1.40
ATOMS15the atoms involved for each of the torsions you wish to calculate=434,454,457,459 REFERENCE15the reference values for each of the torsional angles=2.97
ATOMS16the atoms involved for each of the torsions you wish to calculate=459,487,490,492 REFERENCE16the reference values for each of the torsional angles=2.97
ATOMS17the atoms involved for each of the torsions you wish to calculate=492,511,514,516 REFERENCE17the reference values for each of the torsional angles=2.97
ATOMS18the atoms involved for each of the torsions you wish to calculate=516,535,538,540 REFERENCE18the reference values for each of the torsional angles=2.97
ATOMS19the atoms involved for each of the torsions you wish to calculate=540,568,571,573 REFERENCE19the reference values for each of the torsional angles=2.97
ATOMS20the atoms involved for each of the torsions you wish to calculate=573,593,596,598 REFERENCE20the reference values for each of the torsional angles=2.97
ATOMS21the atoms involved for each of the torsions you wish to calculate=598,619,622,624 REFERENCE21the reference values for each of the torsional angles=2.97
ATOMS22the atoms involved for each of the torsions you wish to calculate=624,648,651,653 REFERENCE22the reference values for each of the torsional angles=2.97
ATOMS23the atoms involved for each of the torsions you wish to calculate=653,672,675,677 REFERENCE23the reference values for each of the torsional angles=2.97
ATOMS24the atoms involved for each of the torsions you wish to calculate=677,696,699,701 REFERENCE24the reference values for each of the torsional angles=2.97
ATOMS25the atoms involved for each of the torsions you wish to calculate=701,719,722,724 REFERENCE25the reference values for each of the torsional angles=2.97
ATOMS26the atoms involved for each of the torsions you wish to calculate=724,744,747,749 REFERENCE26the reference values for each of the torsional angles=2.97
ATOMS27the atoms involved for each of the torsions you wish to calculate=749,770,773,775 REFERENCE27the reference values for each of the torsional angles=2.97
ATOMS28the atoms involved for each of the torsions you wish to calculate=775,799,802,804 REFERENCE28the reference values for each of the torsional angles=2.97
ATOMS29the atoms involved for each of the torsions you wish to calculate=454,457,459,487 REFERENCE29the reference values for each of the torsional angles=0
ATOMS30the atoms involved for each of the torsions you wish to calculate=487,490,492,511 REFERENCE30the reference values for each of the torsional angles=0
ATOMS31the atoms involved for each of the torsions you wish to calculate=511,514,516,535 REFERENCE31the reference values for each of the torsional angles=0
ATOMS32the atoms involved for each of the torsions you wish to calculate=535,538,540,568 REFERENCE32the reference values for each of the torsional angles=0
ATOMS33the atoms involved for each of the torsions you wish to calculate=568,571,573,593 REFERENCE33the reference values for each of the torsional angles=0
ATOMS34the atoms involved for each of the torsions you wish to calculate=593,596,598,619 REFERENCE34the reference values for each of the torsional angles=0
ATOMS35the atoms involved for each of the torsions you wish to calculate=619,622,624,648 REFERENCE35the reference values for each of the torsional angles=0
ATOMS36the atoms involved for each of the torsions you wish to calculate=648,651,653,672 REFERENCE36the reference values for each of the torsional angles=0
ATOMS37the atoms involved for each of the torsions you wish to calculate=672,675,677,696 REFERENCE37the reference values for each of the torsional angles=0
ATOMS38the atoms involved for each of the torsions you wish to calculate=696,699,701,719 REFERENCE38the reference values for each of the torsional angles=0
ATOMS39the atoms involved for each of the torsions you wish to calculate=719,722,724,744 REFERENCE39the reference values for each of the torsional angles=0
ATOMS40the atoms involved for each of the torsions you wish to calculate=744,747,749,770 REFERENCE40the reference values for each of the torsional angles=0
ATOMS41the atoms involved for each of the torsions you wish to calculate=770,773,775,799 REFERENCE41the reference values for each of the torsional angles=0
ATOMS42the atoms involved for each of the torsions you wish to calculate=799,802,804,819 REFERENCE42the reference values for each of the torsional angles=0
LABELa label for the action so that its output can be referenced in the input to other actions=AB_2
... ALPHABETA
# --- End of included input --- 
The ALPHABETA action with label AB_2 calculates the following quantities:
 Quantity   
 Description  
AB_2.value
the alpha beta CVMOVINGRESTRAINTAdd a time-dependent, harmonic restraint on one or more variables. More details ...
  ARGthe labels of the scalars on which the bias will act=d,AB_1,AB_2,AB_PHI0,AB_PHI1,AB_PSI0,AB_PSI1,AB_O0,AB_O1
  STEP0This keyword appears multiple times as STEPx with x=0,1,2,=50000    AT0ATx is equal to the position of the restraint at time STEPx=2,28,23,8,6,13,12,6,4       KAPPA0KAPPAx is equal to the value of the force constants at time STEPx=1000,100,100,100,100,100,100,100,100
  STEP1This keyword appears multiple times as STEPx with x=0,1,2,=2550000  AT1ATx is equal to the position of the restraint at time STEPx=4,42,42,14,14,14,14,14,14   KAPPA1KAPPAx is equal to the value of the force constants at time STEPx=2500,1000,1000,1000,1000,1000,1000,1000,1000
  STEP2This keyword appears multiple times as STEPx with x=0,1,2,=8825000                                  KAPPA2KAPPAx is equal to the value of the force constants at time STEPx=0,1000,1000,1000,1000,1000,1000,1000,1000
  STEP3This keyword appears multiple times as STEPx with x=0,1,2,=25100000		                 KAPPA3KAPPAx is equal to the value of the force constants at time STEPx=0,1000,1000,1000,1000,1000,1000,1000,1000
  STEP4This keyword appears multiple times as STEPx with x=0,1,2,=37500000		                 KAPPA4KAPPAx is equal to the value of the force constants at time STEPx=0,0,0,0,0,0,0,0,0
... MOVINGRESTRAINT

PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=* STRIDE the frequency with which the quantities of interest should be output=1000 FILEthe name of the file on which to output these quantities=COLVAR