PLUMED-NEST

Project ID: plumID:21.014
Source: PLUMED-NEST_chignolin/Part1_MetaD_PBMetaD/plumed_PB20.dat
Originally used with PLUMED version: 2.7
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

MOLINFO
This command is used to provide information on the molecules that are present in your system. More details
 
STRUCTURE
a file in pdb format containing a reference structure
=../template.pdb
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
=1-166

psi1: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=
@psi-1
the four atoms that are required to calculate the psi dihedral for residue 1. Click here for more information. 
 
NOPBC
 ignore the periodic boundary conditions when calculating distances
The TORSION action with label psi1 calculates a scalar quantityphi2: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=
@phi-2
the four atoms that are required to calculate the phi dihedral for residue 2. Click here for more information. 
 
NOPBC
 ignore the periodic boundary conditions when calculating distances
The TORSION action with label phi2 calculates a scalar quantitypsi2: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=
@psi-2
the four atoms that are required to calculate the psi dihedral for residue 2. Click here for more information. 
 
NOPBC
 ignore the periodic boundary conditions when calculating distances
The TORSION action with label psi2 calculates a scalar quantityphi3: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=
@phi-3
the four atoms that are required to calculate the phi dihedral for residue 3. Click here for more information. 
 
NOPBC
 ignore the periodic boundary conditions when calculating distances
The TORSION action with label phi3 calculates a scalar quantitypsi3: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=
@psi-3
the four atoms that are required to calculate the psi dihedral for residue 3. Click here for more information. 
 
NOPBC
 ignore the periodic boundary conditions when calculating distances
The TORSION action with label psi3 calculates a scalar quantityphi4: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=
@phi-4
the four atoms that are required to calculate the phi dihedral for residue 4. Click here for more information. 
 
NOPBC
 ignore the periodic boundary conditions when calculating distances
The TORSION action with label phi4 calculates a scalar quantitypsi4: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=
@psi-4
the four atoms that are required to calculate the psi dihedral for residue 4. Click here for more information. 
 
NOPBC
 ignore the periodic boundary conditions when calculating distances
The TORSION action with label psi4 calculates a scalar quantityphi5: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=
@phi-5
the four atoms that are required to calculate the phi dihedral for residue 5. Click here for more information. 
 
NOPBC
 ignore the periodic boundary conditions when calculating distances
The TORSION action with label phi5 calculates a scalar quantitypsi5: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=
@psi-5
the four atoms that are required to calculate the psi dihedral for residue 5. Click here for more information. 
 
NOPBC
 ignore the periodic boundary conditions when calculating distances
The TORSION action with label psi5 calculates a scalar quantityphi6: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=
@phi-6
the four atoms that are required to calculate the phi dihedral for residue 6. Click here for more information. 
 
NOPBC
 ignore the periodic boundary conditions when calculating distances
The TORSION action with label phi6 calculates a scalar quantitypsi6: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=
@psi-6
the four atoms that are required to calculate the psi dihedral for residue 6. Click here for more information. 
 
NOPBC
 ignore the periodic boundary conditions when calculating distances
The TORSION action with label psi6 calculates a scalar quantityphi7: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=
@phi-7
the four atoms that are required to calculate the phi dihedral for residue 7. Click here for more information. 
 
NOPBC
 ignore the periodic boundary conditions when calculating distances
The TORSION action with label phi7 calculates a scalar quantitypsi7: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=
@psi-7
the four atoms that are required to calculate the psi dihedral for residue 7. Click here for more information. 
 
NOPBC
 ignore the periodic boundary conditions when calculating distances
The TORSION action with label psi7 calculates a scalar quantityphi8: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=
@phi-8
the four atoms that are required to calculate the phi dihedral for residue 8. Click here for more information. 
 
NOPBC
 ignore the periodic boundary conditions when calculating distances
The TORSION action with label phi8 calculates a scalar quantitypsi8: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=
@psi-8
the four atoms that are required to calculate the psi dihedral for residue 8. Click here for more information. 
 
NOPBC
 ignore the periodic boundary conditions when calculating distances
The TORSION action with label psi8 calculates a scalar quantityphi9: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=
@phi-9
the four atoms that are required to calculate the phi dihedral for residue 9. Click here for more information. 
 
NOPBC
 ignore the periodic boundary conditions when calculating distances
The TORSION action with label phi9 calculates a scalar quantitypsi9: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=
@psi-9
the four atoms that are required to calculate the psi dihedral for residue 9. Click here for more information. 
 
NOPBC
 ignore the periodic boundary conditions when calculating distances
The TORSION action with label psi9 calculates a scalar quantityphi10: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=
@phi-10
the four atoms that are required to calculate the phi dihedral for residue 10. Click here for more information. 
 
NOPBC
 ignore the periodic boundary conditions when calculating distances
The TORSION action with label phi10 calculates a scalar quantityrg: 
GYRATION
Calculate the radius of gyration, or other properties related to it. More details
 
ATOMS
the group of atoms that you are calculating the Gyration Tensor for
=
@CA-1
the CA atom in residue 1. Click here for more information. 
,
@CA-2
the CA atom in residue 2. Click here for more information. 
,
@CA-3
the CA atom in residue 3. Click here for more information. 
,
@CA-4
the CA atom in residue 4. Click here for more information. 
,
@CA-5
the CA atom in residue 5. Click here for more information. 
,
@CA-6
the CA atom in residue 6. Click here for more information. 
,
@CA-7
the CA atom in residue 7. Click here for more information. 
,
@CA-8
the CA atom in residue 8. Click here for more information. 
,
@CA-9
the CA atom in residue 9. Click here for more information. 
,
@CA-10
the CA atom in residue 10. Click here for more information. 
 
NOPBC
 ignore the periodic boundary conditions when calculating distances
hh: 
ANTIBETARMSD
Probe the antiparallel beta sheet content of your protein structure. More details
 
RESIDUES
this command is used to specify the set of residues that could conceivably form part of the secondary structure
=all 
TYPE
 the manner in which RMSD alignment is performed
=DRMSD 
R_0
The r_0 parameter of the switching function
=0.1 
STRANDS_CUTOFF
If in a segment of protein the two strands are further apart then the calculation of the actual RMSD is skipped as the structure is very far from being beta-sheet like
=1 
NOPBC
 ignore the periodic boundary conditions

The ANTIBETARMSD action with label hh calculates the following quantities:
 Quantity   
 Description  
hh.struct
the vectors containing the rmsd distances between the residues and each of the reference structures
hh.lessthan
the number blocks of residues that have an RMSD from the secondary structure that is less than the thresholdmm: 
PBMETAD
Used to performed Parallel Bias metadynamics. More details
 ... 
ARG
the input for this action is the scalar output from one or more other actions
=psi1,phi2,psi2,phi3,psi3,phi4,psi4,phi5,psi5,phi6,psi6,phi7,psi7,phi8,psi8,phi9,psi9,phi10,rg,hh 
SIGMA_MAX
the upper bounds for the sigmas (in CV units) when using adaptive hills
=0.6,0.6,0.6,0.6,0.6,0.6,0.6,0.6,0.6,0.6,0.6,0.6,0.6,0.6,0.6,0.6,0.6,0.6,0.6,0.6 
SIGMA_MIN
the lower bounds for the sigmas (in CV units) when using adaptive hills
=0.03,0.03,0.03,0.03,0.03,0.03,0.03,0.03,0.03,0.03,0.03,0.03,0.03,0.03,0.03,0.03,0.03,0.03,0.004,0.02 
SIGMA
the widths of the Gaussian hills
=0.015 
ADAPTIVE
use a geometric (=GEOM) or diffusion (=DIFF) based hills width scheme
=GEOM 
GRID_MIN
the lower bounds for the grid
=-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,0.3,0 
GRID_MAX
the upper bounds for the grid
=pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,1.3,3 
HEIGHT
the height of the Gaussian hills, one for all biases
=0.5 
BIASFACTOR
use well tempered metadynamics with this bias factor, one for all biases
=10 
PACE
the frequency for hill addition, one for all biases
=200 
WALKERS_MPI
 Switch on MPI version of multiple walkers - not compatible with WALKERS_* options other than WALKERS_DIR
 
FILE
files in which the lists of added hills are stored, default names are assigned using arguments if FILE is not found
=../HILLS.psi1,../HILLS.phi2,../HILLS.psi2,../HILLS.phi3,../HILLS.psi3,../HILLS.phi4,../HILLS.psi4,../HILLS.phi5,../HILLS.psi5,../HILLS.phi6,../HILLS.psi6,../HILLS.phi7,../HILLS.psi7,../HILLS.phi8,../HILLS.psi8,../HILLS.phi9,../HILLS.psi9,../HILLS.phi10,../HILLS.rg,../HILLS.hh
GRID_WFILES
dump grid for the bias, default names are used if GRID_WSTRIDE is used without GRID_WFILES
=../GRID.psi1,../GRID.phi2,../GRID.psi2,../GRID.phi3,../GRID.psi3,../GRID.phi4,../GRID.psi4,../GRID.phi5,../GRID.psi5,../GRID.phi6,../GRID.psi6,../GRID.phi7,../GRID.psi7,../GRID.phi8,../GRID.psi8,../GRID.phi9,../GRID.psi9,../GRID.phi10,../GRID.rg,../GRID.hh
#GRID_RFILES=../GRID.psi1,../GRID.phi2,../GRID.psi2,../GRID.phi3,../GRID.psi3,../GRID.phi4,../GRID.psi4,../GRID.phi5,../GRID.psi5,../GRID.phi6,../GRID.psi6,../GRID.phi7,../GRID.psi7,../GRID.phi8,../GRID.psi8,../GRID.phi9,../GRID.psi9,../GRID.phi10,../GRID.rg,../GRID.hh
GRID_WSTRIDE
frequency for dumping the grid
=10000
...

The PBMETAD action with label mm calculates the following quantities:
 Quantity   
 Description  
mm.bias
the instantaneous value of the bias potential
PRINT
Print quantities to a file. More details
 
ARG
the input for this action is the scalar output from one or more other actions
=psi1,phi2,psi2,phi3,psi3,phi4,psi4,phi5,psi5,phi6,psi6,phi7,psi7,phi8,psi8,phi9,psi9,phi10,rg,hh,mm.bias 
FILE
the name of the file on which to output these quantities
=COLVAR 
STRIDE
 the frequency with which the quantities of interest should be output
=1000