PLUMED-NEST

Project ID: plumID:24.003
Source: plumed_nest/diff_sequences/CH22/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
=1-636

# 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
=1-304 
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
=280-304 
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
=339-636 
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
=339-364 
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
=614-636 
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
=1,31,64,89,122,148,177,202,225,251,280,339,365,398,423,456,482,511,536,559,585,614 
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
=1,31,64,89,122,148,177,202,225,251,280 
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
=339,365,398,423,456,482,511,536,559,585,614 
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
=31-63 
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
=89-121 
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
=148-176 
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
=202-224 
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
=251-279 
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
=365-397 
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
=423-455 
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
=482-510 
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
=536-558 
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
=585-613 
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
=29,31,59,62
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
=62,64,84,87
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
=87,89,117,120
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
=120,122,143,146
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
=146,148,172,175
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
=175,177,197,200
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
=200,202,220,223
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
=223,225,246,249
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
=249,251,275,278
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
=278,280,300,303

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
=363,365,393,396
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
=396,398,418,421
phi15The TORSION action with label phi15 calculates the following quantities:
 Quantity   
 Type   
 Description  
phi15
scalar
the TORSION involving these atoms: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=421,423,451,454
phi16The TORSION action with label phi16 calculates the following quantities:
 Quantity   
 Type   
 Description  
phi16
scalar
the TORSION involving these atoms: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=454,456,477,480
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
=480,482,506,509
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
=509,511,531,534
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
=534,536,554,557
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
=557,559,580,583
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
=583,585,609,612
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
=612,614,629,632

# 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
=31,59,62,64
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
=64,84,87,89
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
=89,117,120,122
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
=122,143,146,148
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
=148,172,175,177
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
=177,197,200,202
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
=202,220,223,225
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
=225,246,249,251
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
=251,275,278,280

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
=339,360,363,365
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
=365,393,396,398
psi14The TORSION action with label psi14 calculates the following quantities:
 Quantity   
 Type   
 Description  
psi14
scalar
the TORSION involving these atoms: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=398,418,421,423
psi15The TORSION action with label psi15 calculates the following quantities:
 Quantity   
 Type   
 Description  
psi15
scalar
the TORSION involving these atoms: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=423,451,454,456
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
=456,477,480,482
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
=482,506,509,511
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
=511,531,534,536
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
=536,554,557,559
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
=559,580,583,585
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
=585,609,612,614

# 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
=26,29,31,59
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
=59,62,64,84
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
=84,87,89,117
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
=117,120,122,143
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
=143,146,148,172
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
=172,175,177,197
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
=197,200,202,220
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
=220,223,225,246
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
=246,249,251,275
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
=275,278,280,300

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
=360,363,365,393
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
=393,396,398,418
omega15The TORSION action with label omega15 calculates the following quantities:
 Quantity   
 Type   
 Description  
omega15
scalar
the TORSION involving these atoms: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=418,421,423,451
omega16The TORSION action with label omega16 calculates the following quantities:
 Quantity   
 Type   
 Description  
omega16
scalar
the TORSION involving these atoms: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=451,454,456,477
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
=477,480,482,506
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
=506,509,511,531
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
=531,534,536,554
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
=554,557,559,580
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
=580,583,585,609
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
=609,612,614,629

# 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
=59,31,32,35
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
=84,64,65,71
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
=117,89,90,93
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
=143,122,123,129
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
=172,148,149,155
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
=197,177,178,184
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
=220,202,203,209
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
=246,225,226,232
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
=275,251,252,258
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
=300,280,281,287

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
=360,339,340,346
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
=393,365,366,369
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
=418,398,399,405
chi15The TORSION action with label chi15 calculates the following quantities:
 Quantity   
 Type   
 Description  
chi15
scalar
the TORSION involving these atoms: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=451,423,424,427
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
=477,456,457,463
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
=506,482,483,489
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
=531,511,512,518
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
=554,536,537,543
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
=580,559,560,566
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
=609,585,586,592

# 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: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the 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: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=89,90,93,95
chicThe TORSION action with label chic calculates the following quantities:
 Quantity   
 Type   
 Description  
chic
scalar
the TORSION involving these atoms: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=148,149,155,157
chidThe TORSION action with label chid calculates the following quantities:
 Quantity   
 Type   
 Description  
chid
scalar
the TORSION involving these atoms: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=202,203,209,210
chieThe TORSION action with label chie calculates the following quantities:
 Quantity   
 Type   
 Description  
chie
scalar
the TORSION involving these atoms: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=251,252,258,260

chifThe TORSION action with label chif calculates the following quantities:
 Quantity   
 Type   
 Description  
chif
scalar
the TORSION involving these atoms: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=365,366,369,371
chigThe TORSION action with label chig calculates the following quantities:
 Quantity   
 Type   
 Description  
chig
scalar
the TORSION involving these atoms: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=423,424,427,429
chihThe TORSION action with label chih calculates the following quantities:
 Quantity   
 Type   
 Description  
chih
scalar
the TORSION involving these atoms: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=482,483,489,491
chiiThe TORSION action with label chii calculates the following quantities:
 Quantity   
 Type   
 Description  
chii
scalar
the TORSION involving these atoms: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=536,537,543,544
chijThe TORSION action with label chij calculates the following quantities:
 Quantity   
 Type   
 Description  
chij
scalar
the TORSION involving these atoms: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=585,586,592,594

# 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: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the 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: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=90,93,95,96
chifaThe TORSION action with label chifa calculates the following quantities:
 Quantity   
 Type   
 Description  
chifa
scalar
the TORSION involving these atoms: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=366,369,371,372
chigaThe TORSION action with label chiga calculates the following quantities:
 Quantity   
 Type   
 Description  
chiga
scalar
the TORSION involving these atoms: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=424,427,429,430
# --- 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=4,9,9       KAPPA1=2500,2500,2500
#  STEP2=8825000                  KAPPA2=0,2500,2500
#  STEP3=25100000                 KAPPA3=0,2500,2500
#  STEP4=37500000                 KAPPA4=0,0,0
#... 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