Project ID: plumID:19.005
Source: cmyc_alone/plumed/plumed_master.dat
Originally used with PLUMED version: 2.5
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
#SETTINGS NREPLICAS=2
#this is the master_plumed.dat file for metainference metadynamics simulations
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
=../system/template.pdb
# define protein atoms and make molecule whole prot:
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
ATOMS
the numerical indexes for the set of atoms in the group
=1-191
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
=prot
#include file with definition of metadynamics CVs
INCLUDE
Includes an external input file, similar to #include in C preprocessor. More details. Show included file
FILE
file to be included
=meta_cv_plumed.dat

#activate parallel bias metadynamics
PBMETAD
Used to performed Parallel Bias metadynamics. More details
... #activating start
LABEL
a label for the action so that its output can be referenced in the input to other actions
=pbmetad #to print out things
ARG
the input for this action is the scalar output from one or more other actions
=ahelixright,betasheet,ahelixleft,polypro,rgyr,ohbond
PACE
the frequency for hill addition, one for all biases
=500
HEIGHT
the height of the Gaussian hills, one for all biases
=1.2
BIASFACTOR
use well tempered metadynamics with this bias factor, one for all biases
=10
WALKERS_MPI
Switch on MPI version of multiple walkers - not compatible with WALKERS_* options other than WALKERS_DIR
SIGMA
the widths of the Gaussian hills
=1.01,0.89,0.41,0.72,0.05,0.71
FILE
files in which the lists of added hills are stored, default names are assigned using arguments if FILE is not found
=HILLS_ahelixright,HILLS_betasheet,HILLS_ahelixleft,HILLS_polypro,HILLS_rgyr,HILLS_ohbond
GRID_MIN
the lower bounds for the grid
=-2,-2,-2,-2,0.2,0
GRID_MAX
the upper bounds for the grid
=20,20,20,20,1.4,30 #actual min and max are slightly different, but allowing for gaussian distribution around it ... PBMETAD
#include file with definition of experimental CVs
INCLUDE
Includes an external input file, similar to #include in C preprocessor. More details. Show included file
FILE
file to be included
=exp_cv_plumed.dat

# metainference stuff mi_cs_ha:
METAINFERENCE
Calculates the Metainference energy for a set of experimental data. More details
ARG
the input for this action is the scalar output from one or more other actions
=(cs\.ha-.*),pbmetad.bias
PARARG
reference values for the experimental data, these can be provided as arguments without derivatives
=(cs\.expha
REWEIGHT
simple REWEIGHT using the latest ARG as energy
NOISETYPE
functional form of the noise (GAUSS,MGAUSS,OUTLIERS,MOUTLIERS,GENERIC)
=GAUSS
SIGMA0
initial value of the uncertainty parameter
=1.0
SIGMA_MIN
minimum value of the uncertainty parameter
=0.00001
SIGMA_MAX
maximum value of the uncertainty parameter
=10.0
DSIGMA
maximum MC move of the uncertainty parameter
=0.5
SIGMA_MEAN0
starting value for the uncertainty in the mean estimate
=0.645 mi_cs_hn:
METAINFERENCE
Calculates the Metainference energy for a set of experimental data. More details
ARG
the input for this action is the scalar output from one or more other actions
=(cs\.hn-.*),pbmetad.bias
PARARG
reference values for the experimental data, these can be provided as arguments without derivatives
=(cs\.exphn
REWEIGHT
simple REWEIGHT using the latest ARG as energy
NOISETYPE
functional form of the noise (GAUSS,MGAUSS,OUTLIERS,MOUTLIERS,GENERIC)
=GAUSS
SIGMA0
initial value of the uncertainty parameter
=1.0
SIGMA_MIN
minimum value of the uncertainty parameter
=0.00001
SIGMA_MAX
maximum value of the uncertainty parameter
=10.0
DSIGMA
maximum MC move of the uncertainty parameter
=0.5
SIGMA_MEAN0
starting value for the uncertainty in the mean estimate
=0.645 mi_cs_ca:
METAINFERENCE
Calculates the Metainference energy for a set of experimental data. More details
ARG
the input for this action is the scalar output from one or more other actions
=(cs\.ca-.*),pbmetad.bias
PARARG
reference values for the experimental data, these can be provided as arguments without derivatives
=(cs\.expca
REWEIGHT
simple REWEIGHT using the latest ARG as energy
NOISETYPE
functional form of the noise (GAUSS,MGAUSS,OUTLIERS,MOUTLIERS,GENERIC)
=GAUSS
SIGMA0
initial value of the uncertainty parameter
=1.0
SIGMA_MIN
minimum value of the uncertainty parameter
=0.00001
SIGMA_MAX
maximum value of the uncertainty parameter
=10.0
DSIGMA
maximum MC move of the uncertainty parameter
=0.5
SIGMA_MEAN0
starting value for the uncertainty in the mean estimate
=0.645 mi_cs_cb:
METAINFERENCE
Calculates the Metainference energy for a set of experimental data. More details
ARG
the input for this action is the scalar output from one or more other actions
=(cs\.cb-.*),pbmetad.bias
PARARG
reference values for the experimental data, these can be provided as arguments without derivatives
=(cs\.expcb
REWEIGHT
simple REWEIGHT using the latest ARG as energy
NOISETYPE
functional form of the noise (GAUSS,MGAUSS,OUTLIERS,MOUTLIERS,GENERIC)
=GAUSS
SIGMA0
initial value of the uncertainty parameter
=1.0
SIGMA_MIN
minimum value of the uncertainty parameter
=0.00001
SIGMA_MAX
maximum value of the uncertainty parameter
=10.0
DSIGMA
maximum MC move of the uncertainty parameter
=0.5
SIGMA_MEAN0
starting value for the uncertainty in the mean estimate
=0.645
#print out relavant info
PRINT
Print quantities to a file. More details
STRIDE
the frequency with which the quantities of interest should be output
=200
ARG
the input for this action is the scalar output from one or more other actions
=ahelixright,betasheet,ahelixleft,polypro,rgyr,ohbond,pbmetad.bias
FILE
the name of the file on which to output these quantities
=COLVAR_PBMETAD
PRINT
Print quantities to a file. More details
STRIDE
the frequency with which the quantities of interest should be output
=200
ARG
the input for this action is the scalar output from one or more other actions
=mi_cs_ha.*,mi_cs_hn.*,mi_cs_ca.*,mi_cs_cb
FILE
the name of the file on which to output these quantities
=COLVAR_MI