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 onv2.10
tested onmaster
#SETTINGS NREPLICAS=2
#this is the master_plumed.dat file for metainference metadynamics simulations
MOLINFOThis command is used to provide information on the molecules that are present in your system. More details STRUCTUREa file in pdb format containing a reference structure=../system/template.pdb

# define protein atoms and make molecule whole
prot: GROUPDefine 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 ATOMSthe numerical indexes for the set of atoms in the group=1-191
WHOLEMOLECULESThis action is used to rebuild molecules that can become split by the periodic boundary conditions. More details ENTITY0the atoms that make up a molecule that you wish to align=prot

#include file with definition of metadynamics CVs
INCLUDEIncludes an external input file, similar to #include in C preprocessor. More details. Show included file FILEfile to be included=meta_cv_plumed.dat

#activate parallel bias metadynamics 
PBMETADUsed to performed Parallel Bias metadynamics. More details ... #activating start
LABELa label for the action so that its output can be referenced in the input to other actions=pbmetad #to print out things
ARGthe labels of the scalars on which the bias will act=ahelixright,betasheet,ahelixleft,polypro,rgyr,ohbond
PACEthe frequency for hill addition, one for all biases=500 HEIGHTthe height of the Gaussian hills, one for all biases=1.2 BIASFACTORuse 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 
SIGMAthe widths of the Gaussian hills=1.01,0.89,0.41,0.72,0.05,0.71
FILEfiles 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_MINthe lower bounds for the grid=-2,-2,-2,-2,0.2,0
GRID_MAXthe 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
INCLUDEIncludes an external input file, similar to #include in C preprocessor. More details. Show included file FILEfile to be included=exp_cv_plumed.dat

# metainference stuff
mi_cs_ha: METAINFERENCECalculates the Metainference energy for a set of experimental data. More details ARGthe labels of the scalars on which the bias will act=(cs\.ha-.*),pbmetad.bias PARARGreference 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 DSIGMAmaximum MC move of the uncertainty parameter=0.5 SIGMA_MEAN0starting value for the uncertainty in the mean estimate=0.645
mi_cs_hn: METAINFERENCECalculates the Metainference energy for a set of experimental data. More details ARGthe labels of the scalars on which the bias will act=(cs\.hn-.*),pbmetad.bias PARARGreference 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 DSIGMAmaximum MC move of the uncertainty parameter=0.5 SIGMA_MEAN0starting value for the uncertainty in the mean estimate=0.645
mi_cs_ca: METAINFERENCECalculates the Metainference energy for a set of experimental data. More details ARGthe labels of the scalars on which the bias will act=(cs\.ca-.*),pbmetad.bias PARARGreference 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 DSIGMAmaximum MC move of the uncertainty parameter=0.5 SIGMA_MEAN0starting value for the uncertainty in the mean estimate=0.645
mi_cs_cb: METAINFERENCECalculates the Metainference energy for a set of experimental data. More details ARGthe labels of the scalars on which the bias will act=(cs\.cb-.*),pbmetad.bias PARARGreference 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 DSIGMAmaximum MC move of the uncertainty parameter=0.5 SIGMA_MEAN0starting value for the uncertainty in the mean estimate=0.645

#print out relavant info
PRINTPrint quantities to a file. More details STRIDE the frequency with which the quantities of interest should be output=200 ARGthe labels of the values that you would like to print to the file=ahelixright,betasheet,ahelixleft,polypro,rgyr,ohbond,pbmetad.bias FILEthe name of the file on which to output these quantities=COLVAR_PBMETAD
PRINTPrint quantities to a file. More details STRIDE the frequency with which the quantities of interest should be output=200 ARGthe labels of the values that you would like to print to the file=mi_cs_ha.*,mi_cs_hn.*,mi_cs_ca.*,mi_cs_cb.* FILEthe name of the file on which to output these quantities=COLVAR_MI