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
#SETTINGS NREPLICAS=2 #this is the master_plumed.dat file for metainference metadynamics simulationsMOLINFOThis command is used to provide information on the molecules that are present in your system. More detailsSTRUCTURE=../system/template.pdba file in pdb format containing a reference structure
# 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 detailsATOMS=1-191the numerical indexes for the set of atoms in the groupWHOLEMOLECULESThis action is used to rebuild molecules that can become split by the periodic boundary conditions. More detailsENTITY0=protthe atoms that make up a molecule that you wish to align
#include file with definition of metadynamics CVsINCLUDEIncludes an external input file, similar to #include in C preprocessor. More details. Show included fileFILE=meta_cv_plumed.datfile to be included
#activate parallel bias metadynamicsPBMETAD... #activating startUsed to performed Parallel Bias metadynamics. More detailsLABEL=pbmetad #to print out thingsa label for the action so that its output can be referenced in the input to other actionsARG=ahelixright,betasheet,ahelixleft,polypro,rgyr,ohbondthe input for this action is the scalar output from one or more other actionsPACE=500the frequency for hill addition, one for all biasesHEIGHT=1.2the height of the Gaussian hills, one for all biasesBIASFACTOR=10use well tempered metadynamics with this bias factor, one for all biasesWALKERS_MPISwitch on MPI version of multiple walkers - not compatible with WALKERS_* options other than WALKERS_DIRSIGMA=1.01,0.89,0.41,0.72,0.05,0.71the widths of the Gaussian hillsFILE=HILLS_ahelixright,HILLS_betasheet,HILLS_ahelixleft,HILLS_polypro,HILLS_rgyr,HILLS_ohbondfiles in which the lists of added hills are stored, default names are assigned using arguments if FILE is not foundGRID_MIN=-2,-2,-2,-2,0.2,0the lower bounds for the gridGRID_MAX=20,20,20,20,1.4,30 #actual min and max are slightly different, but allowing for gaussian distribution around it ... PBMETADthe upper bounds for the grid
#include file with definition of experimental CVsINCLUDEIncludes an external input file, similar to #include in C preprocessor. More details. Show included fileFILE=exp_cv_plumed.datfile to be included
# metainference stuff mi_cs_ha:METAINFERENCECalculates the Metainference energy for a set of experimental data. More detailsARG=(cs\.ha-.*),pbmetad.biasthe input for this action is the scalar output from one or more other actionsPARARG=(cs\.exphareference values for the experimental data, these can be provided as arguments without derivativesREWEIGHTsimple REWEIGHT using the latest ARG as energyNOISETYPE=GAUSSfunctional form of the noise (GAUSS,MGAUSS,OUTLIERS,MOUTLIERS,GENERIC)SIGMA0=1.0initial value of the uncertainty parameterSIGMA_MIN=0.00001minimum value of the uncertainty parameterSIGMA_MAX=10.0maximum value of the uncertainty parameterDSIGMA=0.5maximum MC move of the uncertainty parameterSIGMA_MEAN0=0.645 mi_cs_hn:starting value for the uncertainty in the mean estimateMETAINFERENCECalculates the Metainference energy for a set of experimental data. More detailsARG=(cs\.hn-.*),pbmetad.biasthe input for this action is the scalar output from one or more other actionsPARARG=(cs\.exphnreference values for the experimental data, these can be provided as arguments without derivativesREWEIGHTsimple REWEIGHT using the latest ARG as energyNOISETYPE=GAUSSfunctional form of the noise (GAUSS,MGAUSS,OUTLIERS,MOUTLIERS,GENERIC)SIGMA0=1.0initial value of the uncertainty parameterSIGMA_MIN=0.00001minimum value of the uncertainty parameterSIGMA_MAX=10.0maximum value of the uncertainty parameterDSIGMA=0.5maximum MC move of the uncertainty parameterSIGMA_MEAN0=0.645 mi_cs_ca:starting value for the uncertainty in the mean estimateMETAINFERENCECalculates the Metainference energy for a set of experimental data. More detailsARG=(cs\.ca-.*),pbmetad.biasthe input for this action is the scalar output from one or more other actionsPARARG=(cs\.expcareference values for the experimental data, these can be provided as arguments without derivativesREWEIGHTsimple REWEIGHT using the latest ARG as energyNOISETYPE=GAUSSfunctional form of the noise (GAUSS,MGAUSS,OUTLIERS,MOUTLIERS,GENERIC)SIGMA0=1.0initial value of the uncertainty parameterSIGMA_MIN=0.00001minimum value of the uncertainty parameterSIGMA_MAX=10.0maximum value of the uncertainty parameterDSIGMA=0.5maximum MC move of the uncertainty parameterSIGMA_MEAN0=0.645 mi_cs_cb:starting value for the uncertainty in the mean estimateMETAINFERENCECalculates the Metainference energy for a set of experimental data. More detailsARG=(cs\.cb-.*),pbmetad.biasthe input for this action is the scalar output from one or more other actionsPARARG=(cs\.expcbreference values for the experimental data, these can be provided as arguments without derivativesREWEIGHTsimple REWEIGHT using the latest ARG as energyNOISETYPE=GAUSSfunctional form of the noise (GAUSS,MGAUSS,OUTLIERS,MOUTLIERS,GENERIC)SIGMA0=1.0initial value of the uncertainty parameterSIGMA_MIN=0.00001minimum value of the uncertainty parameterSIGMA_MAX=10.0maximum value of the uncertainty parameterDSIGMA=0.5maximum MC move of the uncertainty parameterSIGMA_MEAN0=0.645starting value for the uncertainty in the mean estimate
#print out relavant infoPrint quantities to a file. More detailsSTRIDE=200the frequency with which the quantities of interest should be outputARG=ahelixright,betasheet,ahelixleft,polypro,rgyr,ohbond,pbmetad.biasthe input for this action is the scalar output from one or more other actionsFILE=COLVAR_PBMETADthe name of the file on which to output these quantitiesPrint quantities to a file. More detailsSTRIDE=200the frequency with which the quantities of interest should be outputARG=mi_cs_ha.*,mi_cs_hn.*,mi_cs_ca.*,mi_cs_cbthe input for this action is the scalar output from one or more other actionsFILE=COLVAR_MIthe name of the file on which to output these quantities