Project ID: plumID:21.014
Source: PLUMED-NEST_chignolin/Part1_MetaD_PBMetaD/plumed_PB4.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
tested onv2.9
tested onmaster
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
s1:
CENTER
Calculate the center for a group of atoms, with arbitrary weights. More details
ATOMS
the group of atoms that you are calculating the Gyration Tensor for
=
@back-1
the protein/dna/rna backbone atoms in residue 1. Click here for more information.
NOPBC
ignore the periodic boundary conditions when calculating distances
s2:
CENTER
Calculate the center for a group of atoms, with arbitrary weights. More details
ATOMS
the group of atoms that you are calculating the Gyration Tensor for
=
@back-2
the protein/dna/rna backbone atoms in residue 2. Click here for more information.
NOPBC
ignore the periodic boundary conditions when calculating distances
s3:
CENTER
Calculate the center for a group of atoms, with arbitrary weights. More details
ATOMS
the group of atoms that you are calculating the Gyration Tensor for
=
@back-3
the protein/dna/rna backbone atoms in residue 3. Click here for more information.
NOPBC
ignore the periodic boundary conditions when calculating distances
s4:
CENTER
Calculate the center for a group of atoms, with arbitrary weights. More details
ATOMS
the group of atoms that you are calculating the Gyration Tensor for
=
@back-4
the protein/dna/rna backbone atoms in residue 4. Click here for more information.
NOPBC
ignore the periodic boundary conditions when calculating distances
s5:
CENTER
Calculate the center for a group of atoms, with arbitrary weights. More details
ATOMS
the group of atoms that you are calculating the Gyration Tensor for
=
@back-5
the protein/dna/rna backbone atoms in residue 5. Click here for more information.
NOPBC
ignore the periodic boundary conditions when calculating distances
s6:
CENTER
Calculate the center for a group of atoms, with arbitrary weights. More details
ATOMS
the group of atoms that you are calculating the Gyration Tensor for
=
@back-6
the protein/dna/rna backbone atoms in residue 6. Click here for more information.
NOPBC
ignore the periodic boundary conditions when calculating distances
s7:
CENTER
Calculate the center for a group of atoms, with arbitrary weights. More details
ATOMS
the group of atoms that you are calculating the Gyration Tensor for
=
@back-7
the protein/dna/rna backbone atoms in residue 7. Click here for more information.
NOPBC
ignore the periodic boundary conditions when calculating distances
s8:
CENTER
Calculate the center for a group of atoms, with arbitrary weights. More details
ATOMS
the group of atoms that you are calculating the Gyration Tensor for
=
@back-8
the protein/dna/rna backbone atoms in residue 8. Click here for more information.
NOPBC
ignore the periodic boundary conditions when calculating distances
s9:
CENTER
Calculate the center for a group of atoms, with arbitrary weights. More details
ATOMS
the group of atoms that you are calculating the Gyration Tensor for
=
@back-9
the protein/dna/rna backbone atoms in residue 9. Click here for more information.
NOPBC
ignore the periodic boundary conditions when calculating distances
s10:
CENTER
Calculate the center for a group of atoms, with arbitrary weights. More details
ATOMS
the group of atoms that you are calculating the Gyration Tensor for
=
@back-10
the protein/dna/rna backbone atoms in residue 10. Click here for more information.
NOPBC
ignore the periodic boundary conditions when calculating distances

ALPHABETA
Calculate the alpha beta CV More details
...
NOPBC
ignore the periodic boundary conditions when calculating distances
LABEL
a label for the action so that its output can be referenced in the input to other actions
=back
REFERENCE
the reference values for each of the torsional angles
=0
ATOMS1
the atoms involved for each of the torsions you wish to calculate
=
@psi-1
the four atoms that are required to calculate the psi dihedral for residue 1. Click here for more information.
COEFFICIENT1
the coefficient for each of the torsional angles
=-0.01427455
ATOMS2
the atoms involved for each of the torsions you wish to calculate
=
@phi-2
the four atoms that are required to calculate the phi dihedral for residue 2. Click here for more information.
COEFFICIENT2
the coefficient for each of the torsional angles
=-0.03003557
ATOMS3
the atoms involved for each of the torsions you wish to calculate
=
@psi-2
the four atoms that are required to calculate the psi dihedral for residue 2. Click here for more information.
COEFFICIENT3
the coefficient for each of the torsional angles
=-0.23777775
ATOMS4
the atoms involved for each of the torsions you wish to calculate
=
@phi-3
the four atoms that are required to calculate the phi dihedral for residue 3. Click here for more information.
COEFFICIENT4
the coefficient for each of the torsional angles
=0.139227
ATOMS5
the atoms involved for each of the torsions you wish to calculate
=
@psi-3
the four atoms that are required to calculate the psi dihedral for residue 3. Click here for more information.
COEFFICIENT5
the coefficient for each of the torsional angles
=0.26525215
ATOMS6
the atoms involved for each of the torsions you wish to calculate
=
@phi-4
the four atoms that are required to calculate the phi dihedral for residue 4. Click here for more information.
COEFFICIENT6
the coefficient for each of the torsional angles
=-0.18108167
ATOMS7
the atoms involved for each of the torsions you wish to calculate
=
@psi-4
the four atoms that are required to calculate the psi dihedral for residue 4. Click here for more information.
COEFFICIENT7
the coefficient for each of the torsional angles
=0.01530576
ATOMS8
the atoms involved for each of the torsions you wish to calculate
=
@phi-5
the four atoms that are required to calculate the phi dihedral for residue 5. Click here for more information.
COEFFICIENT8
the coefficient for each of the torsional angles
=0.07231603
ATOMS9
the atoms involved for each of the torsions you wish to calculate
=
@psi-5
the four atoms that are required to calculate the psi dihedral for residue 5. Click here for more information.
COEFFICIENT9
the coefficient for each of the torsional angles
=-0.1183752
ATOMS10
the atoms involved for each of the torsions you wish to calculate
=
@phi-6
the four atoms that are required to calculate the phi dihedral for residue 6. Click here for more information.
COEFFICIENT10
the coefficient for each of the torsional angles
=0.00089293
ATOMS11
the atoms involved for each of the torsions you wish to calculate
=
@psi-6
the four atoms that are required to calculate the psi dihedral for residue 6. Click here for more information.
COEFFICIENT11
the coefficient for each of the torsional angles
=-0.23744683
ATOMS12
the atoms involved for each of the torsions you wish to calculate
=
@phi-7
the four atoms that are required to calculate the phi dihedral for residue 7. Click here for more information.
COEFFICIENT12
the coefficient for each of the torsional angles
=0.15661255
ATOMS13
the atoms involved for each of the torsions you wish to calculate
=
@psi-7
the four atoms that are required to calculate the psi dihedral for residue 7. Click here for more information.
COEFFICIENT13
the coefficient for each of the torsional angles
=0.63855605
ATOMS14
the atoms involved for each of the torsions you wish to calculate
=
@phi-8
the four atoms that are required to calculate the phi dihedral for residue 8. Click here for more information.
COEFFICIENT14
the coefficient for each of the torsional angles
=-0.15161411
ATOMS15
the atoms involved for each of the torsions you wish to calculate
=
@psi-8
the four atoms that are required to calculate the psi dihedral for residue 8. Click here for more information.
COEFFICIENT15
the coefficient for each of the torsional angles
=0.50759965
ATOMS16
the atoms involved for each of the torsions you wish to calculate
=
@phi-9
the four atoms that are required to calculate the phi dihedral for residue 9. Click here for more information.
COEFFICIENT16
the coefficient for each of the torsional angles
=-0.04886669
ATOMS17
the atoms involved for each of the torsions you wish to calculate
=
@psi-9
the four atoms that are required to calculate the psi dihedral for residue 9. Click here for more information.
COEFFICIENT17
the coefficient for each of the torsional angles
=0.13599118
ATOMS18
the atoms involved for each of the torsions you wish to calculate
=
@phi-10
the four atoms that are required to calculate the phi dihedral for residue 10. Click here for more information.
COEFFICIENT18
the coefficient for each of the torsional angles
=-0.1007816 ... cmap:
CONTACTMAP
Calculate the distances between a number of pairs of atoms and transform each distance by a switching function. More details
...
NOPBC
ignore the periodic boundary conditions when calculating distances
SWITCH
The switching functions to use for each of the contacts in your map
={RATIONAL R_0=0.6}
ATOMS1
the atoms involved in each of the contacts you wish to calculate
=s1,s4
WEIGHT1
A weight value for a given contact, by default is 1
=0.02521988
ATOMS2
the atoms involved in each of the contacts you wish to calculate
=s1,s5
WEIGHT2
A weight value for a given contact, by default is 1
=0.20455216
ATOMS3
the atoms involved in each of the contacts you wish to calculate
=s1,s6
WEIGHT3
A weight value for a given contact, by default is 1
=-0.54414755
ATOMS4
the atoms involved in each of the contacts you wish to calculate
=s1,s7
WEIGHT4
A weight value for a given contact, by default is 1
=0.36219968
ATOMS5
the atoms involved in each of the contacts you wish to calculate
=s1,s8
WEIGHT5
A weight value for a given contact, by default is 1
=0.1279484
ATOMS6
the atoms involved in each of the contacts you wish to calculate
=s1,s9
WEIGHT6
A weight value for a given contact, by default is 1
=-0.22453008
ATOMS7
the atoms involved in each of the contacts you wish to calculate
=s1,s10
WEIGHT7
A weight value for a given contact, by default is 1
=0.29550159
ATOMS8
the atoms involved in each of the contacts you wish to calculate
=s2,s5
WEIGHT8
A weight value for a given contact, by default is 1
=-0.03385588
ATOMS9
the atoms involved in each of the contacts you wish to calculate
=s2,s6
WEIGHT9
A weight value for a given contact, by default is 1
=0.09919236
ATOMS10
the atoms involved in each of the contacts you wish to calculate
=s2,s7
WEIGHT10
A weight value for a given contact, by default is 1
=-0.03330457
ATOMS11
the atoms involved in each of the contacts you wish to calculate
=s2,s8
WEIGHT11
A weight value for a given contact, by default is 1
=-0.13847136
ATOMS12
the atoms involved in each of the contacts you wish to calculate
=s2,s9
WEIGHT12
A weight value for a given contact, by default is 1
=0.39094173
ATOMS13
the atoms involved in each of the contacts you wish to calculate
=s2,s10
WEIGHT13
A weight value for a given contact, by default is 1
=-0.1983029
ATOMS14
the atoms involved in each of the contacts you wish to calculate
=s3,s6
WEIGHT14
A weight value for a given contact, by default is 1
=-0.02328201
ATOMS15
the atoms involved in each of the contacts you wish to calculate
=s3,s7
WEIGHT15
A weight value for a given contact, by default is 1
=0.0069981
ATOMS16
the atoms involved in each of the contacts you wish to calculate
=s3,s8
WEIGHT16
A weight value for a given contact, by default is 1
=0.2231250
ATOMS17
the atoms involved in each of the contacts you wish to calculate
=s3,s9
WEIGHT17
A weight value for a given contact, by default is 1
=-0.25618473
ATOMS18
the atoms involved in each of the contacts you wish to calculate
=s3,s10
WEIGHT18
A weight value for a given contact, by default is 1
=0.113674
ATOMS19
the atoms involved in each of the contacts you wish to calculate
=s4,s7
WEIGHT19
A weight value for a given contact, by default is 1
=0.01257499
ATOMS20
the atoms involved in each of the contacts you wish to calculate
=s4,s8
WEIGHT20
A weight value for a given contact, by default is 1
=-0.01498744
ATOMS21
the atoms involved in each of the contacts you wish to calculate
=s4,s9
WEIGHT21
A weight value for a given contact, by default is 1
=-0.11663488
ATOMS22
the atoms involved in each of the contacts you wish to calculate
=s4,s10
WEIGHT22
A weight value for a given contact, by default is 1
=0.084924
ATOMS23
the atoms involved in each of the contacts you wish to calculate
=s5,s8
WEIGHT23
A weight value for a given contact, by default is 1
=-0.005496
ATOMS24
the atoms involved in each of the contacts you wish to calculate
=s5,s9
WEIGHT24
A weight value for a given contact, by default is 1
=0.03150733
ATOMS25
the atoms involved in each of the contacts you wish to calculate
=s5,s10
WEIGHT25
A weight value for a given contact, by default is 1
=-0.03456732
ATOMS26
the atoms involved in each of the contacts you wish to calculate
=s6,s9
WEIGHT26
A weight value for a given contact, by default is 1
=0.00233215
ATOMS27
the atoms involved in each of the contacts you wish to calculate
=s6,s10
WEIGHT27
A weight value for a given contact, by default is 1
=0.01574143
ATOMS28
the atoms involved in each of the contacts you wish to calculate
=s7,s10
WEIGHT28
A weight value for a given contact, by default is 1
=-0.01026257
SUM
calculate the sum of all the contacts in the input
...
rg:
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
=
@N-1
the N atom in residue 1. Click here for more information.
,
@CA-1
the CA atom in residue 1. Click here for more information.
,
@C-1
the C atom in residue 1. Click here for more information.
,
@N-2
the N atom in residue 2. Click here for more information.
,
@CA-2
the CA atom in residue 2. Click here for more information.
,
@C-2
the C atom in residue 2. Click here for more information.
,
@N-3
the N atom in residue 3. Click here for more information.
,
@CA-3
the CA atom in residue 3. Click here for more information.
,
@C-3
the C atom in residue 3. Click here for more information.
,
@N-4
the N atom in residue 4. Click here for more information.
,
@CA-4
the CA atom in residue 4. Click here for more information.
,
@C-4
the C atom in residue 4. Click here for more information.
,
@N-5
the N atom in residue 5. Click here for more information.
,
@CA-5
the CA atom in residue 5. Click here for more information.
,
@C-5
the C atom in residue 5. Click here for more information.
,
@N-6
the N atom in residue 6. Click here for more information.
,
@CA-6
the CA atom in residue 6. Click here for more information.
,
@C-6
the C atom in residue 6. Click here for more information.
,
@N-7
the N atom in residue 7. Click here for more information.
,
@CA-7
the CA atom in residue 7. Click here for more information.
,
@C-7
the C atom in residue 7. Click here for more information.
,
@N-8
the N atom in residue 8. Click here for more information.
,
@CA-8
the CA atom in residue 8. Click here for more information.
,
@C-8
the C atom in residue 8. Click here for more information.
,
@N-9
the N atom in residue 9. Click here for more information.
,
@CA-9
the CA atom in residue 9. Click here for more information.
,
@C-9
the C atom in residue 9. Click here for more information.
,
@N-10
the N atom in residue 10. Click here for more information.
,
@CA-10
the CA atom in residue 10. Click here for more information.
,
@C-10
the C 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

mm:
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
=back,cmap,rg,hh
SIGMA_MAX
the upper bounds for the sigmas (in CV units) when using adaptive hills
=0.2,0.2,0.2,0.2
SIGMA_MIN
the lower bounds for the sigmas (in CV units) when using adaptive hills
=0.01,0.001,0.004,0.02
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
=-4,-2,0.3,0
GRID_MAX
the upper bounds for the grid
=4,2,1.4,3
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.back,../HILLS.cmap,../HILLS.rg,../HILLS.hh
GRID_WFILES
dump grid for the bias, default names are used if GRID_WSTRIDE is used without GRID_WFILES
=../GRID.back,../GRID.cmap,../GRID.rg,../GRID.hh #GRID_RFILES=../GRID.back,../GRID.cmap,../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
=back,cmap,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