PLUMED-NEST

Project ID: plumID:24.003
Source: plumed_nest/diff_sequences/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=p1The COM action with label p1 calculates the following quantities:
 Quantity   
 Type   
 Description  
p1
atoms
virtual atom calculated by COM action
COMCalculate 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=r1The COM action with label r1 calculates the following quantities:
 Quantity   
 Type   
 Description  
r1
atoms
virtual atom calculated by COM action
COMCalculate 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=r14The COM action with label r14 calculates the following quantities:
 Quantity   
 Type   
 Description  
r14
atoms
virtual atom calculated by COM action

# CHAIN TWO AND RESIDUE AFTER LINKER
COMCalculate 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=p2The COM action with label p2 calculates the following quantities:
 Quantity   
 Type   
 Description  
p2
atoms
virtual atom calculated by COM action
COMCalculate 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=r16The COM action with label r16 calculates the following quantities:
 Quantity   
 Type   
 Description  
r16
atoms
virtual atom calculated by COM action
COMCalculate 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=r30The COM action with label r30 calculates the following quantities:
 Quantity   
 Type   
 Description  
r30
atoms
virtual atom calculated by COM action

DISTANCECalculate the distance between a pair 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=dThe DISTANCE action with label d calculates the following quantities:
 Quantity   
 Type   
 Description  
d
scalar
the DISTANCE between this pair of atoms
DISTANCECalculate the distance between a pair 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=inThe DISTANCE action with label in calculates the following quantities:
 Quantity   
 Type   
 Description  
in
scalar
the DISTANCE between this pair of atoms
DISTANCECalculate the distance between a pair 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=FRETThe DISTANCE action with label FRET calculates the following quantities:
 Quantity   
 Type   
 Description  
FRET
scalar
the DISTANCE between this pair of atoms

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

GYRATIONCalculate the radius of gyration, or other properties related to it. More details TYPE The type of calculation relative to the Gyration Tensor you want to perform=RADIUS ATOMSthe group of atoms that you are calculating the Gyration Tensor for=1,31,64,88,112,145,170,196,225,249,273,296,321,347,376 LABELa label for the action so that its output can be referenced in the input to other actions=rg_1The GYRATION action with label rg_1 calculates the following quantities:
 Quantity   
 Type   
 Description  
rg_1
scalar
the radius of gyration

GYRATIONCalculate the radius of gyration, or other properties related to it. More details TYPE The type of calculation relative to the Gyration Tensor you want to perform=RADIUS ATOMSthe group of atoms that you are calculating the Gyration Tensor for=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_2The GYRATION action with label rg_2 calculates the following quantities:
 Quantity   
 Type   
 Description  
rg_2
scalar
the radius of gyration

# hydrophobic residues 
COMCalculate 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=H1The COM action with label H1 calculates the following quantities:
 Quantity   
 Type   
 Description  
H1
atoms
virtual atom calculated by COM action
COMCalculate 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=H2The COM action with label H2 calculates the following quantities:
 Quantity   
 Type   
 Description  
H2
atoms
virtual atom calculated by COM action 
COMCalculate 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=H3The COM action with label H3 calculates the following quantities:
 Quantity   
 Type   
 Description  
H3
atoms
virtual atom calculated by COM action
COMCalculate 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=H4The COM action with label H4 calculates the following quantities:
 Quantity   
 Type   
 Description  
H4
atoms
virtual atom calculated by COM action
COMCalculate 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=H5The COM action with label H5 calculates the following quantities:
 Quantity   
 Type   
 Description  
H5
atoms
virtual atom calculated by COM action

COMCalculate 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_2The COM action with label H1_2 calculates the following quantities:
 Quantity   
 Type   
 Description  
H1_2
atoms
virtual atom calculated by COM action
COMCalculate 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_2The COM action with label H2_2 calculates the following quantities:
 Quantity   
 Type   
 Description  
H2_2
atoms
virtual atom calculated by COM action
COMCalculate 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_2The COM action with label H3_2 calculates the following quantities:
 Quantity   
 Type   
 Description  
H3_2
atoms
virtual atom calculated by COM action
COMCalculate 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_2The COM action with label H4_2 calculates the following quantities:
 Quantity   
 Type   
 Description  
H4_2
atoms
virtual atom calculated by COM action
COMCalculate 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_2The COM action with label H5_2 calculates the following quantities:
 Quantity   
 Type   
 Description  
H5_2
atoms
virtual atom calculated by COM action

COORDINATIONCalculate coordination numbers. This action has hidden defaults. 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=COORDThe COORDINATION action with label COORD calculates the following quantities:
 Quantity   
 Type   
 Description  
COORD
scalar
the value of the coordination
COORDINATIONCalculate coordination numbers. This action uses the defaults shown here. 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  D_0 The d_0 parameter of the switching function=0.0

COORDINATIONCalculate coordination numbers. This action has hidden defaults. 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=PAIRThe COORDINATION action with label PAIR calculates the following quantities:
 Quantity   
 Type   
 Description  
PAIR
scalar
the value of the coordination
COORDINATIONCalculate coordination numbers. This action uses the defaults shown here. 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  D_0 The d_0 parameter of the switching function=0.0

#INCLUDE FILE=prmsd.dat
INCLUDEIncludes 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 somethingphi1The TORSION action with label phi1 calculates the following quantities:
 Quantity   
 Type   
 Description  
phi1
scalar
the TORSION involving these atoms: TORSIONCalculate a torsional angle. More details ATOMSthe four atoms involved in the torsional angle=29,31,59,62
phi2The TORSION action with label phi2 calculates the following quantities:
 Quantity   
 Type   
 Description  
phi2
scalar
the TORSION involving these atoms: TORSIONCalculate a torsional angle. More details ATOMSthe four atoms involved in the torsional angle=62,64,83,86
phi3The TORSION action with label phi3 calculates the following quantities:
 Quantity   
 Type   
 Description  
phi3
scalar
the TORSION involving these atoms: TORSIONCalculate a torsional angle. More details ATOMSthe four atoms involved in the torsional angle=86,88,107,110
phi4The TORSION action with label phi4 calculates the following quantities:
 Quantity   
 Type   
 Description  
phi4
scalar
the TORSION involving these atoms: TORSIONCalculate a torsional angle. More details ATOMSthe four atoms involved in the torsional angle=110,112,140,143
phi5The TORSION action with label phi5 calculates the following quantities:
 Quantity   
 Type   
 Description  
phi5
scalar
the TORSION involving these atoms: TORSIONCalculate a torsional angle. More details ATOMSthe four atoms involved in the torsional angle=143,145,165,168
phi6The TORSION action with label phi6 calculates the following quantities:
 Quantity   
 Type   
 Description  
phi6
scalar
the TORSION involving these atoms: TORSIONCalculate a torsional angle. More details ATOMSthe four atoms involved in the torsional angle=168,170,191,194
phi7The TORSION action with label phi7 calculates the following quantities:
 Quantity   
 Type   
 Description  
phi7
scalar
the TORSION involving these atoms: TORSIONCalculate a torsional angle. More details ATOMSthe four atoms involved in the torsional angle=194,196,220,223
phi8The TORSION action with label phi8 calculates the following quantities:
 Quantity   
 Type   
 Description  
phi8
scalar
the TORSION involving these atoms: TORSIONCalculate a torsional angle. More details ATOMSthe four atoms involved in the torsional angle=223,225,244,247
phi9The TORSION action with label phi9 calculates the following quantities:
 Quantity   
 Type   
 Description  
phi9
scalar
the TORSION involving these atoms: TORSIONCalculate a torsional angle. More details ATOMSthe four atoms involved in the torsional angle=247,249,268,271
phi10The TORSION action with label phi10 calculates the following quantities:
 Quantity   
 Type   
 Description  
phi10
scalar
the TORSION involving these atoms: TORSIONCalculate a torsional angle. More details ATOMSthe four atoms involved in the torsional angle=271,273,291,294
phi11The TORSION action with label phi11 calculates the following quantities:
 Quantity   
 Type   
 Description  
phi11
scalar
the TORSION involving these atoms: TORSIONCalculate a torsional angle. More details ATOMSthe four atoms involved in the torsional angle=294,296,316,319
phi12The TORSION action with label phi12 calculates the following quantities:
 Quantity   
 Type   
 Description  
phi12
scalar
the TORSION involving these atoms: TORSIONCalculate a torsional angle. More details ATOMSthe four atoms involved in the torsional angle=319,321,342,345
phi13The TORSION action with label phi13 calculates the following quantities:
 Quantity   
 Type   
 Description  
phi13
scalar
the TORSION involving these atoms: TORSIONCalculate a torsional angle. More details ATOMSthe four atoms involved in the torsional angle=345,347,371,374
phi14The TORSION action with label phi14 calculates the following quantities:
 Quantity   
 Type   
 Description  
phi14
scalar
the TORSION involving these atoms: TORSIONCalculate a torsional angle. More details ATOMSthe four atoms involved in the torsional angle=374,376,395,398

phi17The TORSION action with label phi17 calculates the following quantities:
 Quantity   
 Type   
 Description  
phi17
scalar
the TORSION involving these atoms: TORSIONCalculate a torsional angle. More details ATOMSthe four atoms involved in the torsional angle=457,459,487,490
phi18The TORSION action with label phi18 calculates the following quantities:
 Quantity   
 Type   
 Description  
phi18
scalar
the TORSION involving these atoms: TORSIONCalculate a torsional angle. More details ATOMSthe four atoms involved in the torsional angle=490,492,511,514
phi19The TORSION action with label phi19 calculates the following quantities:
 Quantity   
 Type   
 Description  
phi19
scalar
the TORSION involving these atoms: TORSIONCalculate a torsional angle. More details ATOMSthe four atoms involved in the torsional angle=514,516,535,538
phi20The TORSION action with label phi20 calculates the following quantities:
 Quantity   
 Type   
 Description  
phi20
scalar
the TORSION involving these atoms: TORSIONCalculate a torsional angle. More details ATOMSthe four atoms involved in the torsional angle=538,540,568,571
phi21The TORSION action with label phi21 calculates the following quantities:
 Quantity   
 Type   
 Description  
phi21
scalar
the TORSION involving these atoms: TORSIONCalculate a torsional angle. More details ATOMSthe four atoms involved in the torsional angle=571,573,593,596
phi22The TORSION action with label phi22 calculates the following quantities:
 Quantity   
 Type   
 Description  
phi22
scalar
the TORSION involving these atoms: TORSIONCalculate a torsional angle. More details ATOMSthe four atoms involved in the torsional angle=596,598,619,622
phi23The TORSION action with label phi23 calculates the following quantities:
 Quantity   
 Type   
 Description  
phi23
scalar
the TORSION involving these atoms: TORSIONCalculate a torsional angle. More details ATOMSthe four atoms involved in the torsional angle=622,624,648,651
phi24The TORSION action with label phi24 calculates the following quantities:
 Quantity   
 Type   
 Description  
phi24
scalar
the TORSION involving these atoms: TORSIONCalculate a torsional angle. More details ATOMSthe four atoms involved in the torsional angle=651,653,672,675
phi25The TORSION action with label phi25 calculates the following quantities:
 Quantity   
 Type   
 Description  
phi25
scalar
the TORSION involving these atoms: TORSIONCalculate a torsional angle. More details ATOMSthe four atoms involved in the torsional angle=675,677,696,699
phi26The TORSION action with label phi26 calculates the following quantities:
 Quantity   
 Type   
 Description  
phi26
scalar
the TORSION involving these atoms: TORSIONCalculate a torsional angle. More details ATOMSthe four atoms involved in the torsional angle=699,701,719,722
phi27The TORSION action with label phi27 calculates the following quantities:
 Quantity   
 Type   
 Description  
phi27
scalar
the TORSION involving these atoms: TORSIONCalculate a torsional angle. More details ATOMSthe four atoms involved in the torsional angle=722,724,744,747
phi28The TORSION action with label phi28 calculates the following quantities:
 Quantity   
 Type   
 Description  
phi28
scalar
the TORSION involving these atoms: TORSIONCalculate a torsional angle. More details ATOMSthe four atoms involved in the torsional angle=747,749,770,773
phi29The TORSION action with label phi29 calculates the following quantities:
 Quantity   
 Type   
 Description  
phi29
scalar
the TORSION involving these atoms: TORSIONCalculate a torsional angle. More details ATOMSthe four atoms involved in the torsional angle=773,775,799,802
phi30The TORSION action with label phi30 calculates the following quantities:
 Quantity   
 Type   
 Description  
phi30
scalar
the TORSION involving these atoms: TORSIONCalculate a torsional angle. More details ATOMSthe four atoms involved in the torsional angle=802,804,819,822

# psi: NL,CA,CLP,NL+
psi0The TORSION action with label psi0 calculates the following quantities:
 Quantity   
 Type   
 Description  
psi0
scalar
the TORSION involving these atoms: TORSIONCalculate a torsional angle. More details ATOMSthe four atoms involved in the torsional angle=1,26,29,31
psi1The TORSION action with label psi1 calculates the following quantities:
 Quantity   
 Type   
 Description  
psi1
scalar
the TORSION involving these atoms: TORSIONCalculate a torsional angle. More details ATOMSthe four atoms involved in the torsional angle=31,59,62,64
psi2The TORSION action with label psi2 calculates the following quantities:
 Quantity   
 Type   
 Description  
psi2
scalar
the TORSION involving these atoms: TORSIONCalculate a torsional angle. More details ATOMSthe four atoms involved in the torsional angle=64,83,86,88
psi3The TORSION action with label psi3 calculates the following quantities:
 Quantity   
 Type   
 Description  
psi3
scalar
the TORSION involving these atoms: TORSIONCalculate a torsional angle. More details ATOMSthe four atoms involved in the torsional angle=88,107,110,112
psi4The TORSION action with label psi4 calculates the following quantities:
 Quantity   
 Type   
 Description  
psi4
scalar
the TORSION involving these atoms: TORSIONCalculate a torsional angle. More details ATOMSthe four atoms involved in the torsional angle=112,140,143,145
psi5The TORSION action with label psi5 calculates the following quantities:
 Quantity   
 Type   
 Description  
psi5
scalar
the TORSION involving these atoms: TORSIONCalculate a torsional angle. More details ATOMSthe four atoms involved in the torsional angle=145,165,168,170
psi6The TORSION action with label psi6 calculates the following quantities:
 Quantity   
 Type   
 Description  
psi6
scalar
the TORSION involving these atoms: TORSIONCalculate a torsional angle. More details ATOMSthe four atoms involved in the torsional angle=170,191,194,196
psi7The TORSION action with label psi7 calculates the following quantities:
 Quantity   
 Type   
 Description  
psi7
scalar
the TORSION involving these atoms: TORSIONCalculate a torsional angle. More details ATOMSthe four atoms involved in the torsional angle=196,220,223,225
psi8The TORSION action with label psi8 calculates the following quantities:
 Quantity   
 Type   
 Description  
psi8
scalar
the TORSION involving these atoms: TORSIONCalculate a torsional angle. More details ATOMSthe four atoms involved in the torsional angle=225,244,247,249
psi9The TORSION action with label psi9 calculates the following quantities:
 Quantity   
 Type   
 Description  
psi9
scalar
the TORSION involving these atoms: TORSIONCalculate a torsional angle. More details ATOMSthe four atoms involved in the torsional angle=249,268,271,273
psi10The TORSION action with label psi10 calculates the following quantities:
 Quantity   
 Type   
 Description  
psi10
scalar
the TORSION involving these atoms: TORSIONCalculate a torsional angle. More details ATOMSthe four atoms involved in the torsional angle=273,291,294,296
psi11The TORSION action with label psi11 calculates the following quantities:
 Quantity   
 Type   
 Description  
psi11
scalar
the TORSION involving these atoms: TORSIONCalculate a torsional angle. More details ATOMSthe four atoms involved in the torsional angle=296,316,319,321
psi12The TORSION action with label psi12 calculates the following quantities:
 Quantity   
 Type   
 Description  
psi12
scalar
the TORSION involving these atoms: TORSIONCalculate a torsional angle. More details ATOMSthe four atoms involved in the torsional angle=321,342,345,347
psi13The TORSION action with label psi13 calculates the following quantities:
 Quantity   
 Type   
 Description  
psi13
scalar
the TORSION involving these atoms: TORSIONCalculate a torsional angle. More details ATOMSthe four atoms involved in the torsional angle=347,371,374,376

psi16The TORSION action with label psi16 calculates the following quantities:
 Quantity   
 Type   
 Description  
psi16
scalar
the TORSION involving these atoms: TORSIONCalculate a torsional angle. More details ATOMSthe four atoms involved in the torsional angle=434,454,457,459
psi17The TORSION action with label psi17 calculates the following quantities:
 Quantity   
 Type   
 Description  
psi17
scalar
the TORSION involving these atoms: TORSIONCalculate a torsional angle. More details ATOMSthe four atoms involved in the torsional angle=459,487,490,492
psi18The TORSION action with label psi18 calculates the following quantities:
 Quantity   
 Type   
 Description  
psi18
scalar
the TORSION involving these atoms: TORSIONCalculate a torsional angle. More details ATOMSthe four atoms involved in the torsional angle=492,511,514,516
psi19The TORSION action with label psi19 calculates the following quantities:
 Quantity   
 Type   
 Description  
psi19
scalar
the TORSION involving these atoms: TORSIONCalculate a torsional angle. More details ATOMSthe four atoms involved in the torsional angle=516,535,538,540
psi20The TORSION action with label psi20 calculates the following quantities:
 Quantity   
 Type   
 Description  
psi20
scalar
the TORSION involving these atoms: TORSIONCalculate a torsional angle. More details ATOMSthe four atoms involved in the torsional angle=540,568,571,573
psi21The TORSION action with label psi21 calculates the following quantities:
 Quantity   
 Type   
 Description  
psi21
scalar
the TORSION involving these atoms: TORSIONCalculate a torsional angle. More details ATOMSthe four atoms involved in the torsional angle=573,593,596,598
psi22The TORSION action with label psi22 calculates the following quantities:
 Quantity   
 Type   
 Description  
psi22
scalar
the TORSION involving these atoms: TORSIONCalculate a torsional angle. More details ATOMSthe four atoms involved in the torsional angle=598,619,622,624
psi23The TORSION action with label psi23 calculates the following quantities:
 Quantity   
 Type   
 Description  
psi23
scalar
the TORSION involving these atoms: TORSIONCalculate a torsional angle. More details ATOMSthe four atoms involved in the torsional angle=624,648,651,653
psi24The TORSION action with label psi24 calculates the following quantities:
 Quantity   
 Type   
 Description  
psi24
scalar
the TORSION involving these atoms: TORSIONCalculate a torsional angle. More details ATOMSthe four atoms involved in the torsional angle=653,672,675,677
psi25The TORSION action with label psi25 calculates the following quantities:
 Quantity   
 Type   
 Description  
psi25
scalar
the TORSION involving these atoms: TORSIONCalculate a torsional angle. More details ATOMSthe four atoms involved in the torsional angle=677,696,699,701
psi26The TORSION action with label psi26 calculates the following quantities:
 Quantity   
 Type   
 Description  
psi26
scalar
the TORSION involving these atoms: TORSIONCalculate a torsional angle. More details ATOMSthe four atoms involved in the torsional angle=701,719,722,724
psi27The TORSION action with label psi27 calculates the following quantities:
 Quantity   
 Type   
 Description  
psi27
scalar
the TORSION involving these atoms: TORSIONCalculate a torsional angle. More details ATOMSthe four atoms involved in the torsional angle=724,744,747,749
psi28The TORSION action with label psi28 calculates the following quantities:
 Quantity   
 Type   
 Description  
psi28
scalar
the TORSION involving these atoms: TORSIONCalculate a torsional angle. More details ATOMSthe four atoms involved in the torsional angle=749,770,773,775
psi29The TORSION action with label psi29 calculates the following quantities:
 Quantity   
 Type   
 Description  
psi29
scalar
the TORSION involving these atoms: TORSIONCalculate a torsional angle. More details ATOMSthe four atoms involved in the torsional angle=775,799,802,804

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

omega1The TORSION action with label omega1 calculates the following quantities:
 Quantity   
 Type   
 Description  
omega1
scalar
the TORSION involving these atoms: TORSIONCalculate a torsional angle. More details ATOMSthe four atoms involved in the torsional angle=26,29,31,59
omega2The TORSION action with label omega2 calculates the following quantities:
 Quantity   
 Type   
 Description  
omega2
scalar
the TORSION involving these atoms: TORSIONCalculate a torsional angle. More details ATOMSthe four atoms involved in the torsional angle=59,62,64,83
omega3The TORSION action with label omega3 calculates the following quantities:
 Quantity   
 Type   
 Description  
omega3
scalar
the TORSION involving these atoms: TORSIONCalculate a torsional angle. More details ATOMSthe four atoms involved in the torsional angle=83,86,88,107
omega4The TORSION action with label omega4 calculates the following quantities:
 Quantity   
 Type   
 Description  
omega4
scalar
the TORSION involving these atoms: TORSIONCalculate a torsional angle. More details ATOMSthe four atoms involved in the torsional angle=107,110,112,140
omega5The TORSION action with label omega5 calculates the following quantities:
 Quantity   
 Type   
 Description  
omega5
scalar
the TORSION involving these atoms: TORSIONCalculate a torsional angle. More details ATOMSthe four atoms involved in the torsional angle=140,143,145,165
omega6The TORSION action with label omega6 calculates the following quantities:
 Quantity   
 Type   
 Description  
omega6
scalar
the TORSION involving these atoms: TORSIONCalculate a torsional angle. More details ATOMSthe four atoms involved in the torsional angle=165,168,170,191
omega7The TORSION action with label omega7 calculates the following quantities:
 Quantity   
 Type   
 Description  
omega7
scalar
the TORSION involving these atoms: TORSIONCalculate a torsional angle. More details ATOMSthe four atoms involved in the torsional angle=191,194,196,220
omega8The TORSION action with label omega8 calculates the following quantities:
 Quantity   
 Type   
 Description  
omega8
scalar
the TORSION involving these atoms: TORSIONCalculate a torsional angle. More details ATOMSthe four atoms involved in the torsional angle=220,223,225,244
omega9The TORSION action with label omega9 calculates the following quantities:
 Quantity   
 Type   
 Description  
omega9
scalar
the TORSION involving these atoms: TORSIONCalculate a torsional angle. More details ATOMSthe four atoms involved in the torsional angle=244,247,249,268
omega10The TORSION action with label omega10 calculates the following quantities:
 Quantity   
 Type   
 Description  
omega10
scalar
the TORSION involving these atoms: TORSIONCalculate a torsional angle. More details ATOMSthe four atoms involved in the torsional angle=268,271,273,291
omega11The TORSION action with label omega11 calculates the following quantities:
 Quantity   
 Type   
 Description  
omega11
scalar
the TORSION involving these atoms: TORSIONCalculate a torsional angle. More details ATOMSthe four atoms involved in the torsional angle=291,294,296,316
omega12The TORSION action with label omega12 calculates the following quantities:
 Quantity   
 Type   
 Description  
omega12
scalar
the TORSION involving these atoms: TORSIONCalculate a torsional angle. More details ATOMSthe four atoms involved in the torsional angle=316,319,321,342
omega13The TORSION action with label omega13 calculates the following quantities:
 Quantity   
 Type   
 Description  
omega13
scalar
the TORSION involving these atoms: TORSIONCalculate a torsional angle. More details ATOMSthe four atoms involved in the torsional angle=342,345,347,371
omega14The TORSION action with label omega14 calculates the following quantities:
 Quantity   
 Type   
 Description  
omega14
scalar
the TORSION involving these atoms: TORSIONCalculate a torsional angle. More details ATOMSthe four atoms involved in the torsional angle=371,374,376,395

omega17The TORSION action with label omega17 calculates the following quantities:
 Quantity   
 Type   
 Description  
omega17
scalar
the TORSION involving these atoms: TORSIONCalculate a torsional angle. More details ATOMSthe four atoms involved in the torsional angle=454,457,459,487
omega18The TORSION action with label omega18 calculates the following quantities:
 Quantity   
 Type   
 Description  
omega18
scalar
the TORSION involving these atoms: TORSIONCalculate a torsional angle. More details ATOMSthe four atoms involved in the torsional angle=487,490,492,511
omega19The TORSION action with label omega19 calculates the following quantities:
 Quantity   
 Type   
 Description  
omega19
scalar
the TORSION involving these atoms: TORSIONCalculate a torsional angle. More details ATOMSthe four atoms involved in the torsional angle=511,514,516,535
omega20The TORSION action with label omega20 calculates the following quantities:
 Quantity   
 Type   
 Description  
omega20
scalar
the TORSION involving these atoms: TORSIONCalculate a torsional angle. More details ATOMSthe four atoms involved in the torsional angle=535,538,540,568
omega21The TORSION action with label omega21 calculates the following quantities:
 Quantity   
 Type   
 Description  
omega21
scalar
the TORSION involving these atoms: TORSIONCalculate a torsional angle. More details ATOMSthe four atoms involved in the torsional angle=568,571,573,593
omega22The TORSION action with label omega22 calculates the following quantities:
 Quantity   
 Type   
 Description  
omega22
scalar
the TORSION involving these atoms: TORSIONCalculate a torsional angle. More details ATOMSthe four atoms involved in the torsional angle=593,596,598,619
omega23The TORSION action with label omega23 calculates the following quantities:
 Quantity   
 Type   
 Description  
omega23
scalar
the TORSION involving these atoms: TORSIONCalculate a torsional angle. More details ATOMSthe four atoms involved in the torsional angle=619,622,624,648
omega24The TORSION action with label omega24 calculates the following quantities:
 Quantity   
 Type   
 Description  
omega24
scalar
the TORSION involving these atoms: TORSIONCalculate a torsional angle. More details ATOMSthe four atoms involved in the torsional angle=648,651,653,672
omega25The TORSION action with label omega25 calculates the following quantities:
 Quantity   
 Type   
 Description  
omega25
scalar
the TORSION involving these atoms: TORSIONCalculate a torsional angle. More details ATOMSthe four atoms involved in the torsional angle=672,675,677,696
omega26The TORSION action with label omega26 calculates the following quantities:
 Quantity   
 Type   
 Description  
omega26
scalar
the TORSION involving these atoms: TORSIONCalculate a torsional angle. More details ATOMSthe four atoms involved in the torsional angle=696,699,701,719
omega27The TORSION action with label omega27 calculates the following quantities:
 Quantity   
 Type   
 Description  
omega27
scalar
the TORSION involving these atoms: TORSIONCalculate a torsional angle. More details ATOMSthe four atoms involved in the torsional angle=719,722,724,744
omega28The TORSION action with label omega28 calculates the following quantities:
 Quantity   
 Type   
 Description  
omega28
scalar
the TORSION involving these atoms: TORSIONCalculate a torsional angle. More details ATOMSthe four atoms involved in the torsional angle=744,747,749,770
omega29The TORSION action with label omega29 calculates the following quantities:
 Quantity   
 Type   
 Description  
omega29
scalar
the TORSION involving these atoms: TORSIONCalculate a torsional angle. More details ATOMSthe four atoms involved in the torsional angle=770,773,775,799
omega30The TORSION action with label omega30 calculates the following quantities:
 Quantity   
 Type   
 Description  
omega30
scalar
the TORSION involving these atoms: TORSIONCalculate a torsional angle. More details ATOMSthe four atoms involved in the torsional angle=799,802,804,819

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

chi1The TORSION action with label chi1 calculates the following quantities:
 Quantity   
 Type   
 Description  
chi1
scalar
the TORSION involving these atoms: TORSIONCalculate a torsional angle. More details ATOMSthe four atoms involved in the torsional angle=59,31,32,35
chi2The TORSION action with label chi2 calculates the following quantities:
 Quantity   
 Type   
 Description  
chi2
scalar
the TORSION involving these atoms: TORSIONCalculate a torsional angle. More details ATOMSthe four atoms involved in the torsional angle=83,64,65,71
chi3The TORSION action with label chi3 calculates the following quantities:
 Quantity   
 Type   
 Description  
chi3
scalar
the TORSION involving these atoms: TORSIONCalculate a torsional angle. More details ATOMSthe four atoms involved in the torsional angle=107,88,89,95
chi4The TORSION action with label chi4 calculates the following quantities:
 Quantity   
 Type   
 Description  
chi4
scalar
the TORSION involving these atoms: TORSIONCalculate a torsional angle. More details ATOMSthe four atoms involved in the torsional angle=140,112,113,116
chi5The TORSION action with label chi5 calculates the following quantities:
 Quantity   
 Type   
 Description  
chi5
scalar
the TORSION involving these atoms: TORSIONCalculate a torsional angle. More details ATOMSthe four atoms involved in the torsional angle=165,145,146,152
chi6The TORSION action with label chi6 calculates the following quantities:
 Quantity   
 Type   
 Description  
chi6
scalar
the TORSION involving these atoms: TORSIONCalculate a torsional angle. More details ATOMSthe four atoms involved in the torsional angle=191,170,171,177
chi7The TORSION action with label chi7 calculates the following quantities:
 Quantity   
 Type   
 Description  
chi7
scalar
the TORSION involving these atoms: TORSIONCalculate a torsional angle. More details ATOMSthe four atoms involved in the torsional angle=220,196,197,203
chi8The TORSION action with label chi8 calculates the following quantities:
 Quantity   
 Type   
 Description  
chi8
scalar
the TORSION involving these atoms: TORSIONCalculate a torsional angle. More details ATOMSthe four atoms involved in the torsional angle=244,225,226,232
chi9The TORSION action with label chi9 calculates the following quantities:
 Quantity   
 Type   
 Description  
chi9
scalar
the TORSION involving these atoms: TORSIONCalculate a torsional angle. More details ATOMSthe four atoms involved in the torsional angle=268,249,250,256
chi10The TORSION action with label chi10 calculates the following quantities:
 Quantity   
 Type   
 Description  
chi10
scalar
the TORSION involving these atoms: TORSIONCalculate a torsional angle. More details ATOMSthe four atoms involved in the torsional angle=291,273,274,280
chi11The TORSION action with label chi11 calculates the following quantities:
 Quantity   
 Type   
 Description  
chi11
scalar
the TORSION involving these atoms: TORSIONCalculate a torsional angle. More details ATOMSthe four atoms involved in the torsional angle=316,296,297,303
chi12The TORSION action with label chi12 calculates the following quantities:
 Quantity   
 Type   
 Description  
chi12
scalar
the TORSION involving these atoms: TORSIONCalculate a torsional angle. More details ATOMSthe four atoms involved in the torsional angle=342,321,322,328
chi13The TORSION action with label chi13 calculates the following quantities:
 Quantity   
 Type   
 Description  
chi13
scalar
the TORSION involving these atoms: TORSIONCalculate a torsional angle. More details ATOMSthe four atoms involved in the torsional angle=371,347,348,354
chi14The TORSION action with label chi14 calculates the following quantities:
 Quantity   
 Type   
 Description  
chi14
scalar
the TORSION involving these atoms: TORSIONCalculate a torsional angle. More details ATOMSthe four atoms involved in the torsional angle=395,376,377,383

chi16The TORSION action with label chi16 calculates the following quantities:
 Quantity   
 Type   
 Description  
chi16
scalar
the TORSION involving these atoms: TORSIONCalculate a torsional angle. More details ATOMSthe four atoms involved in the torsional angle=454,434,435,441
chi17The TORSION action with label chi17 calculates the following quantities:
 Quantity   
 Type   
 Description  
chi17
scalar
the TORSION involving these atoms: TORSIONCalculate a torsional angle. More details ATOMSthe four atoms involved in the torsional angle=487,459,460,463
chi18The TORSION action with label chi18 calculates the following quantities:
 Quantity   
 Type   
 Description  
chi18
scalar
the TORSION involving these atoms: TORSIONCalculate a torsional angle. More details ATOMSthe four atoms involved in the torsional angle=511,492,493,499
chi19The TORSION action with label chi19 calculates the following quantities:
 Quantity   
 Type   
 Description  
chi19
scalar
the TORSION involving these atoms: TORSIONCalculate a torsional angle. More details ATOMSthe four atoms involved in the torsional angle=535,516,517,523
chi20The TORSION action with label chi20 calculates the following quantities:
 Quantity   
 Type   
 Description  
chi20
scalar
the TORSION involving these atoms: TORSIONCalculate a torsional angle. More details ATOMSthe four atoms involved in the torsional angle=568,540,541,544
chi21The TORSION action with label chi21 calculates the following quantities:
 Quantity   
 Type   
 Description  
chi21
scalar
the TORSION involving these atoms: TORSIONCalculate a torsional angle. More details ATOMSthe four atoms involved in the torsional angle=593,573,574,580
chi22The TORSION action with label chi22 calculates the following quantities:
 Quantity   
 Type   
 Description  
chi22
scalar
the TORSION involving these atoms: TORSIONCalculate a torsional angle. More details ATOMSthe four atoms involved in the torsional angle=619,598,599,605
chi23The TORSION action with label chi23 calculates the following quantities:
 Quantity   
 Type   
 Description  
chi23
scalar
the TORSION involving these atoms: TORSIONCalculate a torsional angle. More details ATOMSthe four atoms involved in the torsional angle=648,624,625,631
chi24The TORSION action with label chi24 calculates the following quantities:
 Quantity   
 Type   
 Description  
chi24
scalar
the TORSION involving these atoms: TORSIONCalculate a torsional angle. More details ATOMSthe four atoms involved in the torsional angle=672,653,654,660
chi25The TORSION action with label chi25 calculates the following quantities:
 Quantity   
 Type   
 Description  
chi25
scalar
the TORSION involving these atoms: TORSIONCalculate a torsional angle. More details ATOMSthe four atoms involved in the torsional angle=696,677,678,684
chi26The TORSION action with label chi26 calculates the following quantities:
 Quantity   
 Type   
 Description  
chi26
scalar
the TORSION involving these atoms: TORSIONCalculate a torsional angle. More details ATOMSthe four atoms involved in the torsional angle=719,701,702,708
chi27The TORSION action with label chi27 calculates the following quantities:
 Quantity   
 Type   
 Description  
chi27
scalar
the TORSION involving these atoms: TORSIONCalculate a torsional angle. More details ATOMSthe four atoms involved in the torsional angle=744,724,725,731
chi28The TORSION action with label chi28 calculates the following quantities:
 Quantity   
 Type   
 Description  
chi28
scalar
the TORSION involving these atoms: TORSIONCalculate a torsional angle. More details ATOMSthe four atoms involved in the torsional angle=770,749,750,756
chi29The TORSION action with label chi29 calculates the following quantities:
 Quantity   
 Type   
 Description  
chi29
scalar
the TORSION involving these atoms: TORSIONCalculate a torsional angle. More details ATOMSthe four atoms involved in the torsional angle=799,775,776,782

# chi 2 dihedral: NL,CB1,CG,CD1
chiaThe TORSION action with label chia calculates the following quantities:
 Quantity   
 Type   
 Description  
chia
scalar
the TORSION involving these atoms: TORSIONCalculate a torsional angle. More details ATOMSthe four atoms involved in the torsional angle=31,32,35,37
chibThe TORSION action with label chib calculates the following quantities:
 Quantity   
 Type   
 Description  
chib
scalar
the TORSION involving these atoms: TORSIONCalculate a torsional angle. More details ATOMSthe four atoms involved in the torsional angle=112,113,116,118
chicThe TORSION action with label chic calculates the following quantities:
 Quantity   
 Type   
 Description  
chic
scalar
the TORSION involving these atoms: TORSIONCalculate a torsional angle. More details ATOMSthe four atoms involved in the torsional angle=196,197,203,205
chidThe TORSION action with label chid calculates the following quantities:
 Quantity   
 Type   
 Description  
chid
scalar
the TORSION involving these atoms: TORSIONCalculate a torsional angle. More details ATOMSthe four atoms involved in the torsional angle=273,274,280,281
chieThe TORSION action with label chie calculates the following quantities:
 Quantity   
 Type   
 Description  
chie
scalar
the TORSION involving these atoms: TORSIONCalculate a torsional angle. More details ATOMSthe four atoms involved in the torsional angle=347,348,354,356

chifThe TORSION action with label chif calculates the following quantities:
 Quantity   
 Type   
 Description  
chif
scalar
the TORSION involving these atoms: TORSIONCalculate a torsional angle. More details ATOMSthe four atoms involved in the torsional angle=459,460,463,465
chigThe TORSION action with label chig calculates the following quantities:
 Quantity   
 Type   
 Description  
chig
scalar
the TORSION involving these atoms: TORSIONCalculate a torsional angle. More details ATOMSthe four atoms involved in the torsional angle=540,541,544,546
chihThe TORSION action with label chih calculates the following quantities:
 Quantity   
 Type   
 Description  
chih
scalar
the TORSION involving these atoms: TORSIONCalculate a torsional angle. More details ATOMSthe four atoms involved in the torsional angle=624,625,631,633
chiiThe TORSION action with label chii calculates the following quantities:
 Quantity   
 Type   
 Description  
chii
scalar
the TORSION involving these atoms: TORSIONCalculate a torsional angle. More details ATOMSthe four atoms involved in the torsional angle=701,702,708,709
chijThe TORSION action with label chij calculates the following quantities:
 Quantity   
 Type   
 Description  
chij
scalar
the TORSION involving these atoms: TORSIONCalculate a torsional angle. More details ATOMSthe four atoms involved in the torsional angle=775,776,782,784

# chi 3 dihedral: CB1, CG, CC, CD1 just for NDPEs
chiaaThe TORSION action with label chiaa calculates the following quantities:
 Quantity   
 Type   
 Description  
chiaa
scalar
the TORSION involving these atoms: TORSIONCalculate a torsional angle. More details ATOMSthe four atoms involved in the torsional angle=32,35,37,38
chibaThe TORSION action with label chiba calculates the following quantities:
 Quantity   
 Type   
 Description  
chiba
scalar
the TORSION involving these atoms: TORSIONCalculate a torsional angle. More details ATOMSthe four atoms involved in the torsional angle=113,116,118,119
chifaThe TORSION action with label chifa calculates the following quantities:
 Quantity   
 Type   
 Description  
chifa
scalar
the TORSION involving these atoms: TORSIONCalculate a torsional angle. More details ATOMSthe four atoms involved in the torsional angle=460,463,465,466
chigaThe TORSION action with label chiga calculates the following quantities:
 Quantity   
 Type   
 Description  
chiga
scalar
the TORSION involving these atoms: TORSIONCalculate a torsional angle. More details ATOMSthe four atoms involved in the torsional angle=541,544,546,547
# --- End of included input --- 
# to ensure passing on PLUMED nest, we've commented out some lines in this file
# needed to run the steered MD. these lines utilize a bespoke CV known as 
# ToidRMSD--check out our previous work to read more about the CV or contact 
# Dr. Jim Pfaendtner at pfaendtner@ncsu.edu for more information

#MOVINGRESTRAINT ...
#  ARG=d,a0,b0
#  STEP0=50000    AT0=2,0.09,0.03  KAPPA0=1000,100,100
#  STEP1=2550000  AT1=4,13,13      KAPPA1=2500,2500,2500
#  STEP2=8825000                   KAPPA2=0,2500,2500
#  STEP3=25100000		  KAPPA3=0,2500,2500
#  STEP4=37500000		  KAPPA4=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