PLUMED-NEST

Project ID: plumID:24.003
Source: plumed_nest/diff_sequences/AN30/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

WHOLEMOLECULES
This action is used to rebuild molecules that can become split by the periodic boundary conditions. More details
 
ENTITY0
the atoms that make up a molecule that you wish to align
=1-549

# CHAIN ONE AND RESIDUE BEFORE LINKER
The WHOLEMOLECULES action with label  calculates something
COM
Calculate the center of mass for a group of atoms. More details
 
ATOMS
the list of atoms which are involved the virtual atom's definition
=1-261 
LABEL
a 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
COM
Calculate the center of mass for a group of atoms. More details
 
ATOMS
the list of atoms which are involved the virtual atom's definition
=1-30 
LABEL
a 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
COM
Calculate the center of mass for a group of atoms. More details
 
ATOMS
the list of atoms which are involved the virtual atom's definition
=245-261 
LABEL
a 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
COM
Calculate the center of mass for a group of atoms. More details
 
ATOMS
the list of atoms which are involved the virtual atom's definition
=296-549 
LABEL
a 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
COM
Calculate the center of mass for a group of atoms. More details
 
ATOMS
the list of atoms which are involved the virtual atom's definition
=296-311 
LABEL
a 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
COM
Calculate the center of mass for a group of atoms. More details
 
ATOMS
the list of atoms which are involved the virtual atom's definition
=527-549 
LABEL
a 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

DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=p1,p2 
LABEL
a 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
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=r14,r16 
LABEL
a 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
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=r1,r30 
LABEL
a 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

GYRATION
Calculate 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 
ATOMS
the group of atoms that you are calculating the Gyration Tensor for
=1,31,47,64,80,97,113,130,146,163,179,196,212,229,245,296,312,329,345,362,378,395,411,428,444,461,477,494,510,527 
LABEL
a 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
GYRATION
Calculate 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 
ATOMS
the group of atoms that you are calculating the Gyration Tensor for
=1,31,47,64,80,97,113,130,146,163,179,196,212,229,245 
LABEL
a 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

GYRATION
Calculate 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 
ATOMS
the group of atoms that you are calculating the Gyration Tensor for
=296,312,329,345,362,378,395,411,428,444,461,477,494,510,527 
LABEL
a 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
COM
Calculate the center of mass for a group of atoms. More details
 
ATOMS
the list of atoms which are involved the virtual atom's definition
=31-46 
LABEL
a 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
COM
Calculate the center of mass for a group of atoms. More details
 
ATOMS
the list of atoms which are involved the virtual atom's definition
=80-96 
LABEL
a 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
COM
Calculate the center of mass for a group of atoms. More details
 
ATOMS
the list of atoms which are involved the virtual atom's definition
=130-145 
LABEL
a 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
COM
Calculate the center of mass for a group of atoms. More details
 
ATOMS
the list of atoms which are involved the virtual atom's definition
=179-195 
LABEL
a 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
COM
Calculate the center of mass for a group of atoms. More details
 
ATOMS
the list of atoms which are involved the virtual atom's definition
=229-244 
LABEL
a 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

COM
Calculate the center of mass for a group of atoms. More details
 
ATOMS
the list of atoms which are involved the virtual atom's definition
=312-328 
LABEL
a 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
COM
Calculate the center of mass for a group of atoms. More details
 
ATOMS
the list of atoms which are involved the virtual atom's definition
=362-377 
LABEL
a 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
COM
Calculate the center of mass for a group of atoms. More details
 
ATOMS
the list of atoms which are involved the virtual atom's definition
=411-427 
LABEL
a 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
COM
Calculate the center of mass for a group of atoms. More details
 
ATOMS
the list of atoms which are involved the virtual atom's definition
=461-476 
LABEL
a 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
COM
Calculate the center of mass for a group of atoms. More details
 
ATOMS
the list of atoms which are involved the virtual atom's definition
=510-526 
LABEL
a 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

COORDINATION
Calculate coordination numbers. This action has hidden defaults. More details
 
GROUPA
First list of atoms
=H1,H2,H3,H4,H5 
GROUPB
Second 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_0
The r_0 parameter of the switching function
=1.9 
NLIST
 Use a neighbor list to speed up the calculation
 
NL_CUTOFF
The cutoff for the neighbor list
=2.2 
NL_STRIDE
The 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 
LABEL
a 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
COORDINATION
Calculate coordination numbers. This action uses the defaults shown here. More details
 
GROUPA
First list of atoms
=H1,H2,H3,H4,H5 
GROUPB
Second 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_0
The r_0 parameter of the switching function
=1.9 
NLIST
 Use a neighbor list to speed up the calculation
 
NL_CUTOFF
The cutoff for the neighbor list
=2.2 
NL_STRIDE
The 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 
LABEL
a 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
COORDINATION
Calculate 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
 
GROUPA
First list of atoms
=H1,H2,H3,H4,H5 
GROUPB
Second 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_0
The r_0 parameter of the switching function
=1.9 
NLIST
 Use a neighbor list to speed up the calculation
 
NL_CUTOFF
The cutoff for the neighbor list
=2.2 
NL_STRIDE
The 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 
LABEL
a 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
COORDINATION
Calculate 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
 
GROUPA
First list of atoms
=H1,H2,H3,H4,H5 
GROUPB
Second 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_0
The r_0 parameter of the switching function
=1.9 
NLIST
 Use a neighbor list to speed up the calculation
 
NL_CUTOFF
The cutoff for the neighbor list
=2.2 
NL_STRIDE
The 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 
LABEL
a 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
INCLUDE
Includes an external input file, similar to #include in C preprocessor. More details. Show included file
 
FILE
file 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: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=29,31,42,45
phi2The TORSION action with label phi2 calculates the following quantities:
 Quantity   
 Type   
 Description  
phi2
scalar
the TORSION involving these atoms: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=45,47,59,62
phi3The TORSION action with label phi3 calculates the following quantities:
 Quantity   
 Type   
 Description  
phi3
scalar
the TORSION involving these atoms: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=62,64,75,78
phi4The TORSION action with label phi4 calculates the following quantities:
 Quantity   
 Type   
 Description  
phi4
scalar
the TORSION involving these atoms: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=78,80,92,95
phi5The TORSION action with label phi5 calculates the following quantities:
 Quantity   
 Type   
 Description  
phi5
scalar
the TORSION involving these atoms: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=95,97,108,111
phi6The TORSION action with label phi6 calculates the following quantities:
 Quantity   
 Type   
 Description  
phi6
scalar
the TORSION involving these atoms: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=111,113,125,128
phi7The TORSION action with label phi7 calculates the following quantities:
 Quantity   
 Type   
 Description  
phi7
scalar
the TORSION involving these atoms: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=128,130,141,144
phi8The TORSION action with label phi8 calculates the following quantities:
 Quantity   
 Type   
 Description  
phi8
scalar
the TORSION involving these atoms: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=144,146,158,161
phi9The TORSION action with label phi9 calculates the following quantities:
 Quantity   
 Type   
 Description  
phi9
scalar
the TORSION involving these atoms: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=161,163,174,177
phi10The TORSION action with label phi10 calculates the following quantities:
 Quantity   
 Type   
 Description  
phi10
scalar
the TORSION involving these atoms: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=177,179,191,194
phi11The TORSION action with label phi11 calculates the following quantities:
 Quantity   
 Type   
 Description  
phi11
scalar
the TORSION involving these atoms: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=194,196,207,210
phi12The TORSION action with label phi12 calculates the following quantities:
 Quantity   
 Type   
 Description  
phi12
scalar
the TORSION involving these atoms: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=210,212,224,227
phi13The TORSION action with label phi13 calculates the following quantities:
 Quantity   
 Type   
 Description  
phi13
scalar
the TORSION involving these atoms: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=227,229,240,243
phi14The TORSION action with label phi14 calculates the following quantities:
 Quantity   
 Type   
 Description  
phi14
scalar
the TORSION involving these atoms: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=243,245,257,260

phi17The TORSION action with label phi17 calculates the following quantities:
 Quantity   
 Type   
 Description  
phi17
scalar
the TORSION involving these atoms: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=310,312,324,327
phi18The TORSION action with label phi18 calculates the following quantities:
 Quantity   
 Type   
 Description  
phi18
scalar
the TORSION involving these atoms: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=327,329,340,343
phi19The TORSION action with label phi19 calculates the following quantities:
 Quantity   
 Type   
 Description  
phi19
scalar
the TORSION involving these atoms: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=343,345,357,360
phi20The TORSION action with label phi20 calculates the following quantities:
 Quantity   
 Type   
 Description  
phi20
scalar
the TORSION involving these atoms: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=360,362,373,376
phi21The TORSION action with label phi21 calculates the following quantities:
 Quantity   
 Type   
 Description  
phi21
scalar
the TORSION involving these atoms: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=376,378,390,393
phi22The TORSION action with label phi22 calculates the following quantities:
 Quantity   
 Type   
 Description  
phi22
scalar
the TORSION involving these atoms: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=393,395,406,409
phi23The TORSION action with label phi23 calculates the following quantities:
 Quantity   
 Type   
 Description  
phi23
scalar
the TORSION involving these atoms: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=409,411,423,426
phi24The TORSION action with label phi24 calculates the following quantities:
 Quantity   
 Type   
 Description  
phi24
scalar
the TORSION involving these atoms: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=426,428,439,442
phi25The TORSION action with label phi25 calculates the following quantities:
 Quantity   
 Type   
 Description  
phi25
scalar
the TORSION involving these atoms: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=442,444,456,459
phi26The TORSION action with label phi26 calculates the following quantities:
 Quantity   
 Type   
 Description  
phi26
scalar
the TORSION involving these atoms: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=459,461,472,475
phi27The TORSION action with label phi27 calculates the following quantities:
 Quantity   
 Type   
 Description  
phi27
scalar
the TORSION involving these atoms: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=475,477,489,492
phi28The TORSION action with label phi28 calculates the following quantities:
 Quantity   
 Type   
 Description  
phi28
scalar
the TORSION involving these atoms: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=492,494,505,508
phi29The TORSION action with label phi29 calculates the following quantities:
 Quantity   
 Type   
 Description  
phi29
scalar
the TORSION involving these atoms: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=508,510,522,525
phi30The TORSION action with label phi30 calculates the following quantities:
 Quantity   
 Type   
 Description  
phi30
scalar
the TORSION involving these atoms: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=525,527,542,545

# 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: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the 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: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=31,42,45,47
psi2The TORSION action with label psi2 calculates the following quantities:
 Quantity   
 Type   
 Description  
psi2
scalar
the TORSION involving these atoms: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=47,59,62,64
psi3The TORSION action with label psi3 calculates the following quantities:
 Quantity   
 Type   
 Description  
psi3
scalar
the TORSION involving these atoms: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=64,75,78,80
psi4The TORSION action with label psi4 calculates the following quantities:
 Quantity   
 Type   
 Description  
psi4
scalar
the TORSION involving these atoms: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=80,92,95,97
psi5The TORSION action with label psi5 calculates the following quantities:
 Quantity   
 Type   
 Description  
psi5
scalar
the TORSION involving these atoms: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=97,108,111,113
psi6The TORSION action with label psi6 calculates the following quantities:
 Quantity   
 Type   
 Description  
psi6
scalar
the TORSION involving these atoms: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=113,125,128,130
psi7The TORSION action with label psi7 calculates the following quantities:
 Quantity   
 Type   
 Description  
psi7
scalar
the TORSION involving these atoms: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=130,141,144,146
psi8The TORSION action with label psi8 calculates the following quantities:
 Quantity   
 Type   
 Description  
psi8
scalar
the TORSION involving these atoms: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=146,158,161,163
psi9The TORSION action with label psi9 calculates the following quantities:
 Quantity   
 Type   
 Description  
psi9
scalar
the TORSION involving these atoms: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=163,174,177,179
psi10The TORSION action with label psi10 calculates the following quantities:
 Quantity   
 Type   
 Description  
psi10
scalar
the TORSION involving these atoms: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=179,191,194,196
psi11The TORSION action with label psi11 calculates the following quantities:
 Quantity   
 Type   
 Description  
psi11
scalar
the TORSION involving these atoms: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=196,207,210,212
psi12The TORSION action with label psi12 calculates the following quantities:
 Quantity   
 Type   
 Description  
psi12
scalar
the TORSION involving these atoms: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=212,224,227,229
psi13The TORSION action with label psi13 calculates the following quantities:
 Quantity   
 Type   
 Description  
psi13
scalar
the TORSION involving these atoms: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=229,240,243,245

psi16The TORSION action with label psi16 calculates the following quantities:
 Quantity   
 Type   
 Description  
psi16
scalar
the TORSION involving these atoms: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=296,307,310,312
psi17The TORSION action with label psi17 calculates the following quantities:
 Quantity   
 Type   
 Description  
psi17
scalar
the TORSION involving these atoms: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=312,324,327,329
psi18The TORSION action with label psi18 calculates the following quantities:
 Quantity   
 Type   
 Description  
psi18
scalar
the TORSION involving these atoms: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=329,340,343,345
psi19The TORSION action with label psi19 calculates the following quantities:
 Quantity   
 Type   
 Description  
psi19
scalar
the TORSION involving these atoms: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=345,357,360,362
psi20The TORSION action with label psi20 calculates the following quantities:
 Quantity   
 Type   
 Description  
psi20
scalar
the TORSION involving these atoms: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=362,373,376,378
psi21The TORSION action with label psi21 calculates the following quantities:
 Quantity   
 Type   
 Description  
psi21
scalar
the TORSION involving these atoms: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=378,390,393,395
psi22The TORSION action with label psi22 calculates the following quantities:
 Quantity   
 Type   
 Description  
psi22
scalar
the TORSION involving these atoms: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=395,406,409,411
psi23The TORSION action with label psi23 calculates the following quantities:
 Quantity   
 Type   
 Description  
psi23
scalar
the TORSION involving these atoms: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=411,423,426,428
psi24The TORSION action with label psi24 calculates the following quantities:
 Quantity   
 Type   
 Description  
psi24
scalar
the TORSION involving these atoms: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=428,439,442,444
psi25The TORSION action with label psi25 calculates the following quantities:
 Quantity   
 Type   
 Description  
psi25
scalar
the TORSION involving these atoms: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=444,456,459,461
psi26The TORSION action with label psi26 calculates the following quantities:
 Quantity   
 Type   
 Description  
psi26
scalar
the TORSION involving these atoms: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=461,472,475,477
psi27The TORSION action with label psi27 calculates the following quantities:
 Quantity   
 Type   
 Description  
psi27
scalar
the TORSION involving these atoms: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=477,489,492,494
psi28The TORSION action with label psi28 calculates the following quantities:
 Quantity   
 Type   
 Description  
psi28
scalar
the TORSION involving these atoms: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=494,505,508,510
psi29The TORSION action with label psi29 calculates the following quantities:
 Quantity   
 Type   
 Description  
psi29
scalar
the TORSION involving these atoms: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=510,522,525,527

# 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: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=26,29,31,42
omega2The TORSION action with label omega2 calculates the following quantities:
 Quantity   
 Type   
 Description  
omega2
scalar
the TORSION involving these atoms: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=42,45,47,59
omega3The TORSION action with label omega3 calculates the following quantities:
 Quantity   
 Type   
 Description  
omega3
scalar
the TORSION involving these atoms: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=59,62,64,75
omega4The TORSION action with label omega4 calculates the following quantities:
 Quantity   
 Type   
 Description  
omega4
scalar
the TORSION involving these atoms: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=75,78,80,92
omega5The TORSION action with label omega5 calculates the following quantities:
 Quantity   
 Type   
 Description  
omega5
scalar
the TORSION involving these atoms: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=92,95,97,108
omega6The TORSION action with label omega6 calculates the following quantities:
 Quantity   
 Type   
 Description  
omega6
scalar
the TORSION involving these atoms: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=108,111,113,125
omega7The TORSION action with label omega7 calculates the following quantities:
 Quantity   
 Type   
 Description  
omega7
scalar
the TORSION involving these atoms: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=125,128,130,141
omega8The TORSION action with label omega8 calculates the following quantities:
 Quantity   
 Type   
 Description  
omega8
scalar
the TORSION involving these atoms: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=141,144,146,158
omega9The TORSION action with label omega9 calculates the following quantities:
 Quantity   
 Type   
 Description  
omega9
scalar
the TORSION involving these atoms: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=158,161,163,174
omega10The TORSION action with label omega10 calculates the following quantities:
 Quantity   
 Type   
 Description  
omega10
scalar
the TORSION involving these atoms: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=174,177,179,191
omega11The TORSION action with label omega11 calculates the following quantities:
 Quantity   
 Type   
 Description  
omega11
scalar
the TORSION involving these atoms: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=191,194,196,207
omega12The TORSION action with label omega12 calculates the following quantities:
 Quantity   
 Type   
 Description  
omega12
scalar
the TORSION involving these atoms: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=207,210,212,224
omega13The TORSION action with label omega13 calculates the following quantities:
 Quantity   
 Type   
 Description  
omega13
scalar
the TORSION involving these atoms: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=224,227,229,240
omega14The TORSION action with label omega14 calculates the following quantities:
 Quantity   
 Type   
 Description  
omega14
scalar
the TORSION involving these atoms: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=240,243,245,257

omega17The TORSION action with label omega17 calculates the following quantities:
 Quantity   
 Type   
 Description  
omega17
scalar
the TORSION involving these atoms: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=307,310,312,324
omega18The TORSION action with label omega18 calculates the following quantities:
 Quantity   
 Type   
 Description  
omega18
scalar
the TORSION involving these atoms: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=324,327,329,340
omega19The TORSION action with label omega19 calculates the following quantities:
 Quantity   
 Type   
 Description  
omega19
scalar
the TORSION involving these atoms: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=340,343,345,357
omega20The TORSION action with label omega20 calculates the following quantities:
 Quantity   
 Type   
 Description  
omega20
scalar
the TORSION involving these atoms: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=357,360,362,373
omega21The TORSION action with label omega21 calculates the following quantities:
 Quantity   
 Type   
 Description  
omega21
scalar
the TORSION involving these atoms: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=373,376,378,390
omega22The TORSION action with label omega22 calculates the following quantities:
 Quantity   
 Type   
 Description  
omega22
scalar
the TORSION involving these atoms: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=390,393,395,406
omega23The TORSION action with label omega23 calculates the following quantities:
 Quantity   
 Type   
 Description  
omega23
scalar
the TORSION involving these atoms: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=406,409,411,423
omega24The TORSION action with label omega24 calculates the following quantities:
 Quantity   
 Type   
 Description  
omega24
scalar
the TORSION involving these atoms: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=423,426,428,439
omega25The TORSION action with label omega25 calculates the following quantities:
 Quantity   
 Type   
 Description  
omega25
scalar
the TORSION involving these atoms: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=439,442,444,456
omega26The TORSION action with label omega26 calculates the following quantities:
 Quantity   
 Type   
 Description  
omega26
scalar
the TORSION involving these atoms: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=456,459,461,472
omega27The TORSION action with label omega27 calculates the following quantities:
 Quantity   
 Type   
 Description  
omega27
scalar
the TORSION involving these atoms: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=472,475,477,489
omega28The TORSION action with label omega28 calculates the following quantities:
 Quantity   
 Type   
 Description  
omega28
scalar
the TORSION involving these atoms: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=489,492,494,505
omega29The TORSION action with label omega29 calculates the following quantities:
 Quantity   
 Type   
 Description  
omega29
scalar
the TORSION involving these atoms: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=505,508,510,522
omega30The TORSION action with label omega30 calculates the following quantities:
 Quantity   
 Type   
 Description  
omega30
scalar
the TORSION involving these atoms: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=522,525,527,542

# 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: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=42,31,32,35
chi2The TORSION action with label chi2 calculates the following quantities:
 Quantity   
 Type   
 Description  
chi2
scalar
the TORSION involving these atoms: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=59,47,48,51
chi3The TORSION action with label chi3 calculates the following quantities:
 Quantity   
 Type   
 Description  
chi3
scalar
the TORSION involving these atoms: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=75,64,65,68
chi4The TORSION action with label chi4 calculates the following quantities:
 Quantity   
 Type   
 Description  
chi4
scalar
the TORSION involving these atoms: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=92,80,81,84
chi5The TORSION action with label chi5 calculates the following quantities:
 Quantity   
 Type   
 Description  
chi5
scalar
the TORSION involving these atoms: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=108,97,98,101
chi6The TORSION action with label chi6 calculates the following quantities:
 Quantity   
 Type   
 Description  
chi6
scalar
the TORSION involving these atoms: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=125,113,114,117
chi7The TORSION action with label chi7 calculates the following quantities:
 Quantity   
 Type   
 Description  
chi7
scalar
the TORSION involving these atoms: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=141,130,131,134
chi8The TORSION action with label chi8 calculates the following quantities:
 Quantity   
 Type   
 Description  
chi8
scalar
the TORSION involving these atoms: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=158,146,147,150
chi9The TORSION action with label chi9 calculates the following quantities:
 Quantity   
 Type   
 Description  
chi9
scalar
the TORSION involving these atoms: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=174,163,164,167
chi10The TORSION action with label chi10 calculates the following quantities:
 Quantity   
 Type   
 Description  
chi10
scalar
the TORSION involving these atoms: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=191,179,180,183
chi11The TORSION action with label chi11 calculates the following quantities:
 Quantity   
 Type   
 Description  
chi11
scalar
the TORSION involving these atoms: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=207,196,197,200
chi12The TORSION action with label chi12 calculates the following quantities:
 Quantity   
 Type   
 Description  
chi12
scalar
the TORSION involving these atoms: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=224,212,213,216
chi13The TORSION action with label chi13 calculates the following quantities:
 Quantity   
 Type   
 Description  
chi13
scalar
the TORSION involving these atoms: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=240,229,230,233
chi14The TORSION action with label chi14 calculates the following quantities:
 Quantity   
 Type   
 Description  
chi14
scalar
the TORSION involving these atoms: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=257,245,246,249

chi16The TORSION action with label chi16 calculates the following quantities:
 Quantity   
 Type   
 Description  
chi16
scalar
the TORSION involving these atoms: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=307,296,297,300
chi17The TORSION action with label chi17 calculates the following quantities:
 Quantity   
 Type   
 Description  
chi17
scalar
the TORSION involving these atoms: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=324,312,313,316
chi18The TORSION action with label chi18 calculates the following quantities:
 Quantity   
 Type   
 Description  
chi18
scalar
the TORSION involving these atoms: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=340,329,330,333
chi19The TORSION action with label chi19 calculates the following quantities:
 Quantity   
 Type   
 Description  
chi19
scalar
the TORSION involving these atoms: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=357,345,346,349
chi20The TORSION action with label chi20 calculates the following quantities:
 Quantity   
 Type   
 Description  
chi20
scalar
the TORSION involving these atoms: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=373,362,363,366
chi21The TORSION action with label chi21 calculates the following quantities:
 Quantity   
 Type   
 Description  
chi21
scalar
the TORSION involving these atoms: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=390,378,379,382
chi22The TORSION action with label chi22 calculates the following quantities:
 Quantity   
 Type   
 Description  
chi22
scalar
the TORSION involving these atoms: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=406,395,396,399
chi23The TORSION action with label chi23 calculates the following quantities:
 Quantity   
 Type   
 Description  
chi23
scalar
the TORSION involving these atoms: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=423,411,412,415
chi24The TORSION action with label chi24 calculates the following quantities:
 Quantity   
 Type   
 Description  
chi24
scalar
the TORSION involving these atoms: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=439,428,429,432
chi25The TORSION action with label chi25 calculates the following quantities:
 Quantity   
 Type   
 Description  
chi25
scalar
the TORSION involving these atoms: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=456,444,445,448
chi26The TORSION action with label chi26 calculates the following quantities:
 Quantity   
 Type   
 Description  
chi26
scalar
the TORSION involving these atoms: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=472,461,462,465
chi27The TORSION action with label chi27 calculates the following quantities:
 Quantity   
 Type   
 Description  
chi27
scalar
the TORSION involving these atoms: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=489,477,478,481
chi28The TORSION action with label chi28 calculates the following quantities:
 Quantity   
 Type   
 Description  
chi28
scalar
the TORSION involving these atoms: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=505,494,495,498
chi29The TORSION action with label chi29 calculates the following quantities:
 Quantity   
 Type   
 Description  
chi29
scalar
the TORSION involving these atoms: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=522,510,511,514
# --- End of included input --- 
MOVINGRESTRAINT
Add a time-dependent, harmonic restraint on one or more variables. More details
 ...
  
ARG
the input for this action is the scalar output from one or more other actions
=d
  
STEP0
This keyword appears multiple times as STEPx with x=0,1,2,
=50000    
AT0
ATx is equal to the position of the restraint at time STEPx
=2  
KAPPA0
KAPPAx is equal to the value of the force constants at time STEPx
=1000
  
STEP1
This keyword appears multiple times as STEPx with x=0,1,2,
=2550000  
AT1
ATx is equal to the position of the restraint at time STEPx
=4  
KAPPA1
KAPPAx is equal to the value of the force constants at time STEPx
=2500
  
STEP2
This keyword appears multiple times as STEPx with x=0,1,2,
=8825000         
KAPPA2
KAPPAx is equal to the value of the force constants at time STEPx
=0
  
STEP3
This keyword appears multiple times as STEPx with x=0,1,2,
=25100000        
KAPPA3
KAPPAx is equal to the value of the force constants at time STEPx
=0
  
STEP4
This keyword appears multiple times as STEPx with x=0,1,2,
=37500000        
KAPPA4
KAPPAx is equal to the value of the force constants at time STEPx
=0
... MOVINGRESTRAINT

PRINT
Print quantities to a file. More details
 
ARG
the input for this action is the scalar output from one or more other actions
 
STRIDE
 the frequency with which the quantities of interest should be output
=1000 
FILE
the name of the file on which to output these quantities
=COLVAR