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
=p1
The COM action with label p1 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
=1-30 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=r1
The COM action with label r1 calculates 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
=280-304 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=r14

# CHAIN TWO AND RESIDUE AFTER LINKER
The COM action with label r14 calculates 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
=339-636 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=p2
The COM action with label p2 calculates 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
=339-364 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=r16
The COM action with label r16 calculates 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
=614-636 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=r30

The COM action with label r30 calculates something
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
=d
The DISTANCE action with label d calculates the following quantities:
 Quantity   
 Description  
d.value
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
=in
The DISTANCE action with label in calculates the following quantities:
 Quantity   
 Description  
in.value
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
=FRET

The DISTANCE action with label FRET calculates the following quantities:
 Quantity   
 Description  
FRET.value
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
=rg
The GYRATION action with label rg calculates something
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_1

The GYRATION action with label rg_1 calculates something
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_2

# hydrophobic residues
The GYRATION action with label rg_2 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
=31-63 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=H1
The COM action with label H1 calculates 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
=89-121 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=H2
The COM action with label H2 calculates 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
=148-176 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=H3
The COM action with label H3 calculates 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
=202-224 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=H4
The COM action with label H4 calculates 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
=251-279 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=H5

The COM action with label H5 calculates 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
=365-397 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=H1_2
The COM action with label H1_2 calculates 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
=423-455 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=H2_2
The COM action with label H2_2 calculates 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
=482-510 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=H3_2
The COM action with label H3_2 calculates 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
=536-558 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=H4_2
The COM action with label H4_2 calculates 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
=585-613 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=H5_2

The COM action with label H5_2 calculates something
COORDINATION
Calculate coordination numbers. 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
The COORDINATION action with label COORD calculates the following quantities:
 Quantity   
 Description  
COORD.value
the value of the coordination
COORDINATION
Calculate coordination numbers. 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

#INCLUDE FILE=prmsd.dat
The COORDINATION action with label PAIR calculates the following quantities:
 Quantity   
 Description  
PAIR.value
the value of the coordination
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 somethingphi1: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=29,31,59,62
The TORSION action with label phi1 calculates the following quantities:
 Quantity   
 Description  
phi1.value
the TORSION involving these atomsphi2: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=62,64,84,87
The TORSION action with label phi2 calculates the following quantities:
 Quantity   
 Description  
phi2.value
the TORSION involving these atomsphi3: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=87,89,117,120
The TORSION action with label phi3 calculates the following quantities:
 Quantity   
 Description  
phi3.value
the TORSION involving these atomsphi4: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=120,122,143,146
The TORSION action with label phi4 calculates the following quantities:
 Quantity   
 Description  
phi4.value
the TORSION involving these atomsphi5: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=146,148,172,175
The TORSION action with label phi5 calculates the following quantities:
 Quantity   
 Description  
phi5.value
the TORSION involving these atomsphi6: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=175,177,197,200
The TORSION action with label phi6 calculates the following quantities:
 Quantity   
 Description  
phi6.value
the TORSION involving these atomsphi7: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=200,202,220,223
The TORSION action with label phi7 calculates the following quantities:
 Quantity   
 Description  
phi7.value
the TORSION involving these atomsphi8: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=223,225,246,249
The TORSION action with label phi8 calculates the following quantities:
 Quantity   
 Description  
phi8.value
the TORSION involving these atomsphi9: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=249,251,275,278
The TORSION action with label phi9 calculates the following quantities:
 Quantity   
 Description  
phi9.value
the TORSION involving these atomsphi10: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=278,280,300,303

The TORSION action with label phi10 calculates the following quantities:
 Quantity   
 Description  
phi10.value
the TORSION involving these atomsphi13: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=363,365,393,396
The TORSION action with label phi13 calculates the following quantities:
 Quantity   
 Description  
phi13.value
the TORSION involving these atomsphi14: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=396,398,418,421
The TORSION action with label phi14 calculates the following quantities:
 Quantity   
 Description  
phi14.value
the TORSION involving these atomsphi15: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=421,423,451,454
The TORSION action with label phi15 calculates the following quantities:
 Quantity   
 Description  
phi15.value
the TORSION involving these atomsphi16: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=454,456,477,480
The TORSION action with label phi16 calculates the following quantities:
 Quantity   
 Description  
phi16.value
the TORSION involving these atomsphi17: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=480,482,506,509
The TORSION action with label phi17 calculates the following quantities:
 Quantity   
 Description  
phi17.value
the TORSION involving these atomsphi18: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=509,511,531,534
The TORSION action with label phi18 calculates the following quantities:
 Quantity   
 Description  
phi18.value
the TORSION involving these atomsphi19: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=534,536,554,557
The TORSION action with label phi19 calculates the following quantities:
 Quantity   
 Description  
phi19.value
the TORSION involving these atomsphi20: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=557,559,580,583
The TORSION action with label phi20 calculates the following quantities:
 Quantity   
 Description  
phi20.value
the TORSION involving these atomsphi21: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=583,585,609,612
The TORSION action with label phi21 calculates the following quantities:
 Quantity   
 Description  
phi21.value
the TORSION involving these atomsphi22: 
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+

The TORSION action with label phi22 calculates the following quantities:
 Quantity   
 Description  
phi22.value
the TORSION involving these atomspsi0: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=1,26,29,31
The TORSION action with label psi0 calculates the following quantities:
 Quantity   
 Description  
psi0.value
the TORSION involving these atomspsi1: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=31,59,62,64
The TORSION action with label psi1 calculates the following quantities:
 Quantity   
 Description  
psi1.value
the TORSION involving these atomspsi2: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=64,84,87,89
The TORSION action with label psi2 calculates the following quantities:
 Quantity   
 Description  
psi2.value
the TORSION involving these atomspsi3: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=89,117,120,122
The TORSION action with label psi3 calculates the following quantities:
 Quantity   
 Description  
psi3.value
the TORSION involving these atomspsi4: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=122,143,146,148
The TORSION action with label psi4 calculates the following quantities:
 Quantity   
 Description  
psi4.value
the TORSION involving these atomspsi5: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=148,172,175,177
The TORSION action with label psi5 calculates the following quantities:
 Quantity   
 Description  
psi5.value
the TORSION involving these atomspsi6: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=177,197,200,202
The TORSION action with label psi6 calculates the following quantities:
 Quantity   
 Description  
psi6.value
the TORSION involving these atomspsi7: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=202,220,223,225
The TORSION action with label psi7 calculates the following quantities:
 Quantity   
 Description  
psi7.value
the TORSION involving these atomspsi8: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=225,246,249,251
The TORSION action with label psi8 calculates the following quantities:
 Quantity   
 Description  
psi8.value
the TORSION involving these atomspsi9: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=251,275,278,280

The TORSION action with label psi9 calculates the following quantities:
 Quantity   
 Description  
psi9.value
the TORSION involving these atomspsi12: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=339,360,363,365
The TORSION action with label psi12 calculates the following quantities:
 Quantity   
 Description  
psi12.value
the TORSION involving these atomspsi13: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=365,393,396,398
The TORSION action with label psi13 calculates the following quantities:
 Quantity   
 Description  
psi13.value
the TORSION involving these atomspsi14: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=398,418,421,423
The TORSION action with label psi14 calculates the following quantities:
 Quantity   
 Description  
psi14.value
the TORSION involving these atomspsi15: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=423,451,454,456
The TORSION action with label psi15 calculates the following quantities:
 Quantity   
 Description  
psi15.value
the TORSION involving these atomspsi16: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=456,477,480,482
The TORSION action with label psi16 calculates the following quantities:
 Quantity   
 Description  
psi16.value
the TORSION involving these atomspsi17: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=482,506,509,511
The TORSION action with label psi17 calculates the following quantities:
 Quantity   
 Description  
psi17.value
the TORSION involving these atomspsi18: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=511,531,534,536
The TORSION action with label psi18 calculates the following quantities:
 Quantity   
 Description  
psi18.value
the TORSION involving these atomspsi19: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=536,554,557,559
The TORSION action with label psi19 calculates the following quantities:
 Quantity   
 Description  
psi19.value
the TORSION involving these atomspsi20: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=559,580,583,585
The TORSION action with label psi20 calculates the following quantities:
 Quantity   
 Description  
psi20.value
the TORSION involving these atomspsi21: 
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

The TORSION action with label psi21 calculates the following quantities:
 Quantity   
 Description  
psi21.value
the TORSION involving these atomsomega1: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=26,29,31,59
The TORSION action with label omega1 calculates the following quantities:
 Quantity   
 Description  
omega1.value
the TORSION involving these atomsomega2: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=59,62,64,84
The TORSION action with label omega2 calculates the following quantities:
 Quantity   
 Description  
omega2.value
the TORSION involving these atomsomega3: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=84,87,89,117
The TORSION action with label omega3 calculates the following quantities:
 Quantity   
 Description  
omega3.value
the TORSION involving these atomsomega4: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=117,120,122,143
The TORSION action with label omega4 calculates the following quantities:
 Quantity   
 Description  
omega4.value
the TORSION involving these atomsomega5: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=143,146,148,172
The TORSION action with label omega5 calculates the following quantities:
 Quantity   
 Description  
omega5.value
the TORSION involving these atomsomega6: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=172,175,177,197
The TORSION action with label omega6 calculates the following quantities:
 Quantity   
 Description  
omega6.value
the TORSION involving these atomsomega7: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=197,200,202,220
The TORSION action with label omega7 calculates the following quantities:
 Quantity   
 Description  
omega7.value
the TORSION involving these atomsomega8: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=220,223,225,246
The TORSION action with label omega8 calculates the following quantities:
 Quantity   
 Description  
omega8.value
the TORSION involving these atomsomega9: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=246,249,251,275
The TORSION action with label omega9 calculates the following quantities:
 Quantity   
 Description  
omega9.value
the TORSION involving these atomsomega10: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=275,278,280,300

The TORSION action with label omega10 calculates the following quantities:
 Quantity   
 Description  
omega10.value
the TORSION involving these atomsomega13: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=360,363,365,393
The TORSION action with label omega13 calculates the following quantities:
 Quantity   
 Description  
omega13.value
the TORSION involving these atomsomega14: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=393,396,398,418
The TORSION action with label omega14 calculates the following quantities:
 Quantity   
 Description  
omega14.value
the TORSION involving these atomsomega15: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=418,421,423,451
The TORSION action with label omega15 calculates the following quantities:
 Quantity   
 Description  
omega15.value
the TORSION involving these atomsomega16: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=451,454,456,477
The TORSION action with label omega16 calculates the following quantities:
 Quantity   
 Description  
omega16.value
the TORSION involving these atomsomega17: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=477,480,482,506
The TORSION action with label omega17 calculates the following quantities:
 Quantity   
 Description  
omega17.value
the TORSION involving these atomsomega18: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=506,509,511,531
The TORSION action with label omega18 calculates the following quantities:
 Quantity   
 Description  
omega18.value
the TORSION involving these atomsomega19: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=531,534,536,554
The TORSION action with label omega19 calculates the following quantities:
 Quantity   
 Description  
omega19.value
the TORSION involving these atomsomega20: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=554,557,559,580
The TORSION action with label omega20 calculates the following quantities:
 Quantity   
 Description  
omega20.value
the TORSION involving these atomsomega21: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=580,583,585,609
The TORSION action with label omega21 calculates the following quantities:
 Quantity   
 Description  
omega21.value
the TORSION involving these atomsomega22: 
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)

The TORSION action with label omega22 calculates the following quantities:
 Quantity   
 Description  
omega22.value
the TORSION involving these atomschi1: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=59,31,32,35
The TORSION action with label chi1 calculates the following quantities:
 Quantity   
 Description  
chi1.value
the TORSION involving these atomschi2: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=84,64,65,71
The TORSION action with label chi2 calculates the following quantities:
 Quantity   
 Description  
chi2.value
the TORSION involving these atomschi3: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=117,89,90,93
The TORSION action with label chi3 calculates the following quantities:
 Quantity   
 Description  
chi3.value
the TORSION involving these atomschi4: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=143,122,123,129
The TORSION action with label chi4 calculates the following quantities:
 Quantity   
 Description  
chi4.value
the TORSION involving these atomschi5: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=172,148,149,155
The TORSION action with label chi5 calculates the following quantities:
 Quantity   
 Description  
chi5.value
the TORSION involving these atomschi6: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=197,177,178,184
The TORSION action with label chi6 calculates the following quantities:
 Quantity   
 Description  
chi6.value
the TORSION involving these atomschi7: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=220,202,203,209
The TORSION action with label chi7 calculates the following quantities:
 Quantity   
 Description  
chi7.value
the TORSION involving these atomschi8: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=246,225,226,232
The TORSION action with label chi8 calculates the following quantities:
 Quantity   
 Description  
chi8.value
the TORSION involving these atomschi9: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=275,251,252,258
The TORSION action with label chi9 calculates the following quantities:
 Quantity   
 Description  
chi9.value
the TORSION involving these atomschi10: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=300,280,281,287

The TORSION action with label chi10 calculates the following quantities:
 Quantity   
 Description  
chi10.value
the TORSION involving these atomschi12: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=360,339,340,346
The TORSION action with label chi12 calculates the following quantities:
 Quantity   
 Description  
chi12.value
the TORSION involving these atomschi13: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=393,365,366,369
The TORSION action with label chi13 calculates the following quantities:
 Quantity   
 Description  
chi13.value
the TORSION involving these atomschi14: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=418,398,399,405
The TORSION action with label chi14 calculates the following quantities:
 Quantity   
 Description  
chi14.value
the TORSION involving these atomschi15: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=451,423,424,427
The TORSION action with label chi15 calculates the following quantities:
 Quantity   
 Description  
chi15.value
the TORSION involving these atomschi16: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=477,456,457,463
The TORSION action with label chi16 calculates the following quantities:
 Quantity   
 Description  
chi16.value
the TORSION involving these atomschi17: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=506,482,483,489
The TORSION action with label chi17 calculates the following quantities:
 Quantity   
 Description  
chi17.value
the TORSION involving these atomschi18: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=531,511,512,518
The TORSION action with label chi18 calculates the following quantities:
 Quantity   
 Description  
chi18.value
the TORSION involving these atomschi19: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=554,536,537,543
The TORSION action with label chi19 calculates the following quantities:
 Quantity   
 Description  
chi19.value
the TORSION involving these atomschi20: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=580,559,560,566
The TORSION action with label chi20 calculates the following quantities:
 Quantity   
 Description  
chi20.value
the TORSION involving these atomschi21: 
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
The TORSION action with label chi21 calculates the following quantities:
 Quantity   
 Description  
chi21.value
the TORSION involving these atomschia: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=31,32,35,37
The TORSION action with label chia calculates the following quantities:
 Quantity   
 Description  
chia.value
the TORSION involving these atomschib: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=89,90,93,95
The TORSION action with label chib calculates the following quantities:
 Quantity   
 Description  
chib.value
the TORSION involving these atomschic: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=148,149,155,157
The TORSION action with label chic calculates the following quantities:
 Quantity   
 Description  
chic.value
the TORSION involving these atomschid: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=202,203,209,210
The TORSION action with label chid calculates the following quantities:
 Quantity   
 Description  
chid.value
the TORSION involving these atomschie: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=251,252,258,260

The TORSION action with label chie calculates the following quantities:
 Quantity   
 Description  
chie.value
the TORSION involving these atomschif: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=365,366,369,371
The TORSION action with label chif calculates the following quantities:
 Quantity   
 Description  
chif.value
the TORSION involving these atomschig: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=423,424,427,429
The TORSION action with label chig calculates the following quantities:
 Quantity   
 Description  
chig.value
the TORSION involving these atomschih: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=482,483,489,491
The TORSION action with label chih calculates the following quantities:
 Quantity   
 Description  
chih.value
the TORSION involving these atomschii: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=536,537,543,544
The TORSION action with label chii calculates the following quantities:
 Quantity   
 Description  
chii.value
the TORSION involving these atomschij: 
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
The TORSION action with label chij calculates the following quantities:
 Quantity   
 Description  
chij.value
the TORSION involving these atomschiaa: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=32,35,37,38
The TORSION action with label chiaa calculates the following quantities:
 Quantity   
 Description  
chiaa.value
the TORSION involving these atomschiba: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=90,93,95,96
The TORSION action with label chiba calculates the following quantities:
 Quantity   
 Description  
chiba.value
the TORSION involving these atomschifa: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=366,369,371,372
The TORSION action with label chifa calculates the following quantities:
 Quantity   
 Description  
chifa.value
the TORSION involving these atomschiga: 
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

The TORSION action with label chiga calculates the following quantities:
 Quantity   
 Description  
chiga.value
the TORSION involving these atoms
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