PLUMED-NEST

Project ID: plumID:21.040
Source: PRODUCTION/plumed.dat
Originally used with PLUMED version: 2.6
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

RESTART
Activate restart. More details

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
=structure.pdb
# define all heavy atoms using GROMACS index file
# which can be created with gmx_mpi make_ndx
protein-h: 
GROUP
Define a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details
 
NDX_FILE
the name of index file (gromacs syntax)
=index.ndx 
NDX_GROUP
the name of the group to be imported (gromacs syntax) - first group found is used by default
=Protein-H
protein: 
GROUP
Define a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details
 
NDX_FILE
the name of index file (gromacs syntax)
=index.ndx 
NDX_GROUP
the name of the group to be imported (gromacs syntax) - first group found is used by default
=Protein
Protein-noASPGLU-noH: 
GROUP
Define a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details
 
NDX_FILE
the name of index file (gromacs syntax)
=index.ndx 
NDX_GROUP
the name of the group to be imported (gromacs syntax) - first group found is used by default
=no_ASP_GLU_no_OE1_OE2_OD1_OD2_Protein-H
system: 
GROUP
Define a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details
 
NDX_FILE
the name of index file (gromacs syntax)
=index.ndx 
NDX_GROUP
the name of the group to be imported (gromacs syntax) - first group found is used by default
=System
beta1: 
GROUP
Define a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details
 
NDX_FILE
the name of index file (gromacs syntax)
=index.ndx 
NDX_GROUP
the name of the group to be imported (gromacs syntax) - first group found is used by default
=beta1
beta2: 
GROUP
Define a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details
 
NDX_FILE
the name of index file (gromacs syntax)
=index.ndx 
NDX_GROUP
the name of the group to be imported (gromacs syntax) - first group found is used by default
=beta2
beta3: 
GROUP
Define a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details
 
NDX_FILE
the name of index file (gromacs syntax)
=index.ndx 
NDX_GROUP
the name of the group to be imported (gromacs syntax) - first group found is used by default
=beta3
beta4: 
GROUP
Define a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details
 
NDX_FILE
the name of index file (gromacs syntax)
=index.ndx 
NDX_GROUP
the name of the group to be imported (gromacs syntax) - first group found is used by default
=beta4

50_48: 
GROUP
Define a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details
 
NDX_FILE
the name of index file (gromacs syntax)
=index.ndx 
NDX_GROUP
the name of the group to be imported (gromacs syntax) - first group found is used by default
=50_48
78_80: 
GROUP
Define a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details
 
NDX_FILE
the name of index file (gromacs syntax)
=index.ndx 
NDX_GROUP
the name of the group to be imported (gromacs syntax) - first group found is used by default
=78_80
109_111: 
GROUP
Define a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details
 
NDX_FILE
the name of index file (gromacs syntax)
=index.ndx 
NDX_GROUP
the name of the group to be imported (gromacs syntax) - first group found is used by default
=109_111
140_142: 
GROUP
Define a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details
 
NDX_FILE
the name of index file (gromacs syntax)
=index.ndx 
NDX_GROUP
the name of the group to be imported (gromacs syntax) - first group found is used by default
=140_142

beta1_com: 
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
=beta1
beta2_com: 
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
=beta2
beta3_com: 
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
=beta3
beta4_com: 
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
=beta4

50_48_com: 
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
=50_48
78_80_com: 
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
=78_80
109_111_com: 
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
=109_111
140_142_com: 
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
=140_142

distance1: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=beta1_com,50_48_com
The DISTANCE action with label distance1 calculates a scalar quantitydistance2: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=beta2_com,78_80_com
The DISTANCE action with label distance2 calculates a scalar quantitydistance3: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=beta3_com,109_111_com
The DISTANCE action with label distance3 calculates a scalar quantitydistance4: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=beta4_com,140_142_com

#plus 1.3 
The DISTANCE action with label distance4 calculates a scalar quantity
UPPER_WALLS
Defines a wall for the value of one or more collective variables, More details
 
ARG
the arguments on which the bias is acting
=distance1 
AT
the positions of the wall
=4.2 
KAPPA
the force constant for the wall
=100 
EXP
 the powers for the walls
=2 
OFFSET
 the offset for the start of the wall
=0 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=uwall1
UPPER_WALLS
Defines a wall for the value of one or more collective variables, More details
 
ARG
the arguments on which the bias is acting
=distance2 
AT
the positions of the wall
=4.2 
KAPPA
the force constant for the wall
=100 
EXP
 the powers for the walls
=2 
OFFSET
 the offset for the start of the wall
=0 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=uwall2
UPPER_WALLS
Defines a wall for the value of one or more collective variables, More details
 
ARG
the arguments on which the bias is acting
=distance3 
AT
the positions of the wall
=4.2 
KAPPA
the force constant for the wall
=100 
EXP
 the powers for the walls
=2 
OFFSET
 the offset for the start of the wall
=0 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=uwall3
UPPER_WALLS
Defines a wall for the value of one or more collective variables, More details
 
ARG
the arguments on which the bias is acting
=distance4 
AT
the positions of the wall
=4.2 
KAPPA
the force constant for the wall
=100 
EXP
 the powers for the walls
=2 
OFFSET
 the offset for the start of the wall
=0 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=uwall4

# make protein whole: add reference position of first heavy atom (in nm)
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
=1-6840 
ENTITY1
the atoms that make up a molecule that you wish to align
=6841-6880 
ENTITY2
the atoms that make up a molecule that you wish to align
=6881-13814 
ENTITY3
the atoms that make up a molecule that you wish to align
=13815-13859 
ENTITY4
the atoms that make up a molecule that you wish to align
=13860-20699 
ENTITY5
the atoms that make up a molecule that you wish to align
=20700-20739 
ENTITY6
the atoms that make up a molecule that you wish to align
=20740-27673 
ENTITY7
the atoms that make up a molecule that you wish to align
=27674-27718 
ENTITY8
the atoms that make up a molecule that you wish to align
=27719-34558 
ENTITY9
the atoms that make up a molecule that you wish to align
=34559-34598 
ENTITY10
the atoms that make up a molecule that you wish to align
=34599-41532 
ENTITY11
the atoms that make up a molecule that you wish to align
=41533-41577 
ENTITY12
the atoms that make up a molecule that you wish to align
=41578-48417 
ENTITY13
the atoms that make up a molecule that you wish to align
=48418-48457 
ENTITY14
the atoms that make up a molecule that you wish to align
=48458-55391 
ENTITY15
the atoms that make up a molecule that you wish to align
=55392-55436 
ENTITY16
the atoms that make up a molecule that you wish to align
=55437-62276 
ENTITY17
the atoms that make up a molecule that you wish to align
=62277-62316 
ENTITY18
the atoms that make up a molecule that you wish to align
=62317-69250 
ENTITY19
the atoms that make up a molecule that you wish to align
=69251-69295 
ENTITY20
the atoms that make up a molecule that you wish to align
=69296-76135 
ENTITY21
the atoms that make up a molecule that you wish to align
=76136-76175 
ENTITY22
the atoms that make up a molecule that you wish to align
=76176-83109 
ENTITY23
the atoms that make up a molecule that you wish to align
=83110-83154 
ENTITY24
the atoms that make up a molecule that you wish to align
=83155-89994 
ENTITY25
the atoms that make up a molecule that you wish to align
=89995-90034 
ENTITY26
the atoms that make up a molecule that you wish to align
=90035-96968 
ENTITY27
the atoms that make up a molecule that you wish to align
=96969-97013 
ENTITY28
the atoms that make up a molecule that you wish to align
=97014-99997 
ADDREFERENCE
 Define the reference position of the first atom of each entity using a PDB file
 REF0=34.307,44.84,8.469 REF1=35.495,45.583,5.476 REF2=34.303,44.744,12.551 REF3=35.512,45.661,9.382 REF4=34.387,44.82,16.569 REF5=35.575,45.562,13.575 REF6=34.384,44.724,20.65 REF7=35.593,45.641,17.481 REF8=34.468,44.799,24.668 REF9=35.656,45.542,21.675 REF10=34.464,44.703,28.75 REF11=35.673,45.621,25.581 REF12=34.549,44.779,32.768 REF13=35.737,45.521,29.774 REF14=34.545,44.683,36.849 REF15=35.754,45.6,33.68 REF16=34.63,44.758,40.868 REF17=35.818,45.501,37.874 REF18=34.626,44.663,44.949 REF19=35.835,45.58,41.78 REF20=34.71,44.738,48.967 REF21=35.898,45.48,45.973 REF22=34.707,44.642,53.049 REF23=35.915,45.559,49.88 REF24=34.791,44.717,57.067 REF25=35.979,45.46,54.073 REF26=34.787,44.622,61.148 REF27=35.996,45.539,57.979 REF28=37.207,50.967,0.94


# create EMMI score
EMMI
Calculate the fit of a structure or ensemble of structures with a cryo-EM density map. More details
 ...
LABEL
a label for the action so that its output can be referenced in the input to other actions
=gmm 
NOPBC
 ignore the periodic boundary conditions when calculating distances
 
TEMP
temperature
=310.0 
NL_STRIDE
The frequency with which we are updating the neighbor list
=100 
NL_CUTOFF
The cutoff in overlap for the neighbor list
=0.01
ATOMS
atoms for which we calculate the density map, typically all heavy atoms
=Protein-noASPGLU-noH 
GMM_FILE
file with the parameters of the GMM components
=MT_TAU.dat
#ATOMS selects what is refined
# no-negative-no-h or no-h are reasonable
# resolution is not used - no Bfactor fitting
# SIGMA_MIN can go down to 0.02, must be > NL_CUTOFF,
# if crashes, raise back to 0.05,
# the larger the number the softer the contribution of the EM data
SIGMA_MIN
minimum uncertainty
=0.03 
RESOLUTION
Cryo-EM map resolution
=0.1 
NOISETYPE
functional form of the noise (GAUSS, OUTLIERS, MARGINAL)
=MARGINAL
#WRITE_OV=OV_FILE.dat 
#WRITE_OV_STRIDE=500
...
# translate into bias
The EMMI action with label gmm calculates the following quantities:
 Quantity   
 Description  
gmm.scoreb
Bayesian score
gmm.acc
MC acceptance for uncertainty
gmm.sigma
uncertainty in the forward models and experiment
gmm.neff
effective number of replicasemr: 
BIASVALUE
Takes the value of one variable and use it as a bias More details
 
ARG
the input for this action is the scalar output from one or more other actions
=gmm.scoreb 
STRIDE
the frequency with which the forces due to the bias should be calculated
=2
#DUMPMASSCHARGE FILE=mcfile
# print useful info to file
The BIASVALUE action with label emr calculates the following quantities:
 Quantity   
 Description  
emr.bias
the instantaneous value of the bias potential
emr._bias
one or multiple instances of this quantity can be referenced elsewhere in the input file
PRINT
Print quantities to a file. More details
 
ARG
the input for this action is the scalar output from one or more other actions
 
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
=5000