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
The MOLINFO action with label  calculates something
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

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
=
@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
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
=
@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
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
=
@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
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
=
@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
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
=
@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
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
=
@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
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
=
@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
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
=
@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
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
=
@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
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
=
@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
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
=
@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
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
=
@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
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
=
@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
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
=
@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
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
=
@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
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
=
@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
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
=
@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
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
=
@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
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
 
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
hhThe ANTIBETARMSD action with label hh calculates the following quantities:
 Quantity   
 Type   
 Description  
hh
scalar
the value calculated by this action: 
ANTIBETARMSD
Probe the antiparallel beta sheet content of your protein structure. This action is a shortcut and it has hidden defaults. 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
hh: 
ANTIBETARMSD
Probe the antiparallel beta sheet content of your protein structure. This action is a shortcut and uses the defaults shown here. 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
  
NN
 The n parameter of the switching function
=8 
D_0
 The d_0 parameter of the switching function
=0.0 
MM
 The m parameter of the switching function
=12 
STYLE
 Antiparallel beta sheets can either form in a single chain or from a pair of chains
=all
# PLUMED interprets the command:
# hh: ANTIBETARMSD RESIDUES=all TYPE=DRMSD R_0=0.1 STRANDS_CUTOFF=1 NOPBC
# as follows (Click the red comment above to revert to the short version of the input):
hh_rmsdThe SECONDARY_STRUCTURE_RMSD action with label hh_rmsd calculates the following quantities:
 Quantity   
 Type   
 Description  
hh_rmsd
vector
the value calculated by this action: 
SECONDARY_STRUCTURE_RMSD
Calclulate the distance between segments of a protein and a reference structure of interest More details
 
BONDLENGTH
the length to use for bonds
=0.17 
ATOMS
this is the full list of atoms that we are investigating
=1,5,7,22,23,24,26,28,43,44,45,47,49,55,56,57,67,64,69,70,71,73,75,84,85,86,88,90,98,99,100,102,104,105,106,107,109,111,119,120,121,123,125,143,144,145,147,149,164,166 
TYPE
 the manner in which RMSD alignment is performed
=DRMSD 
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
 
SEGMENT1
this is the lists of atoms in the segment that are being considered
=0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39 
SEGMENT2
this is the lists of atoms in the segment that are being considered
=0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44 
SEGMENT3
this is the lists of atoms in the segment that are being considered
=0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49 
SEGMENT4
this is the lists of atoms in the segment that are being considered
=5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44 
SEGMENT5
this is the lists of atoms in the segment that are being considered
=5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49 
STRUCTURE1
the reference structure
=2.263,-3.795,1.722,2.493,-2.426,2.263,3.847,-1.838,1.761,1.301,-1.517,1.921,0.852,-1.504,0.739,0.818,-0.738,2.917,-0.299,0.243,2.748,-1.421,-0.076,3.757,0.273,1.68,2.854,0.902,1.993,3.888,0.119,2.532,1.813,0.683,3.916,1.68,1.58,3.94,0.395,-0.394,5.011,1.63,-1.459,4.814,0.982,-2.962,3.559,-1.359,-2.439,2.526,-2.287,-1.189,3.006,-3.087,-2.081,1.231,-1.52,-1.524,1.324,-0.409,-2.326,0.037,-2.095,-1.858,-1.269,-1.554,-3.053,-2.199,-1.291,-0.869,-1.949,-2.512,-1.255,-2.07,-3.71,0.326,-2.363,-2.072,1.405,-2.992,-2.872,2.699,-2.129,-2.917,1.745,-4.399,-2.33,1.899,-4.545,-1.102     # Action input conctinues with 1 further SEGMENTn keywords, 
hh_ltThe LESS_THAN action with label hh_lt calculates the following quantities:
 Quantity   
 Type   
 Description  
hh_lt
vector
the vector obtained by doing an element-wise application of a function that is one if the input is less than a threshold to the input vectors: 
LESS_THAN
Use a switching function to determine how many of the input variables are less than a certain cutoff. More details
 
ARG
the input to this function
=hh_rmsd 
SWITCH
This keyword is used if you want to employ an alternative to the continuous swiching function defined above
={RATIONAL R_0=0.1 D_0=0.0 NN=8 MM=12} 
hhThe SUM action with label hh calculates the following quantities:
 Quantity   
 Type   
 Description  
hh
scalar
the sum of all the elements in the input vector: 
SUM
Calculate the sum of the arguments More details
 
ARG
the input to this function
=hh_lt 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
# --- End of included input --- 
mmThe PBMETAD action with label mm calculates the following quantities:
 Quantity   
 Type   
 Description  
mm.bias
scalar
the instantaneous value of the bias potential: 
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
...

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