Project ID: plumID:20.014
Source: PLUMED_input_files/AB42_and_10074_G5/plumed/plumed.dat
Originally used with PLUMED version: 2.6.0
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 metadynamic metainference simulations
# define groupsMOLINFOThis 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 structureWHOLEMOLECULESThis action is used to rebuild molecules that can become split by the periodic boundary conditions. More detailsENTITY0=1-627the atoms that make up a molecule that you wish to alignENTITY1=628-664the atoms that make up a molecule that you wish to alignFLUSHThis command instructs plumed to flush all the open files with a user specified frequency. More detailsSTRIDE=1000the frequency with which all the open files should be flushed
#include file with definition of metadynamics CVs on peptideINCLUDEIncludes an external input file, similar to #include in C preprocessor. More details. Show included fileFILE=CVs.datfile to be included
#include file with definition of metadynamics CVs involving the small moleculeINCLUDEIncludes an external input file, similar to #include in C preprocessor. More details. Show included fileFILE=CVs_drug.datfile to be included
# Chemical shifts at 278 KCS2BACKBONECalculates the backbone chemical shifts for a protein. This action has hidden defaults. More detailsATOMS=1-627The atoms to be included in the calculation, eDATADIR=../dataThe folder with the experimental chemical shiftsNOPBCignore the periodic boundary conditions when calculating distancesTEMPLATE=../system/template.pdb cs:A PDB file of the protein system
#activate parallel bias metadynamicsPBMETAD...Used to performed Parallel Bias metadynamics. More detailsARG=helix.lessthan,beta,rgyr,hydro,salt,dihcor,reg1,reg2,reg3,reg4,reg5,reg6,reg7,reg8,reg9,reg10,reg11,reg12,reg13,reg14,ligtor1,ligtor2,ligtor3,ligtor4the input for this action is the scalar output from one or more other actionsHEIGHT=1.2the height of the Gaussian hills, one for all biasesBIASFACTOR=49 #10*SQRT(NUM_OF_CVS)use well tempered metadynamics with this bias factor, one for all biasesSIGMA=0.64,0.33,0.03,0.69,2.75,1.34,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,0.1,0.1,0.1,0.1the widths of the Gaussian hillsPACE=500the frequency for hill addition, one for all biasesGRID_MIN=-1,-1,-1,-1,-1,-1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,-pi,-pi,-pi,-pithe lower bounds for the gridGRID_MAX=100,100,20,200,400,50,150,150,150,150,150,150,150,150,150,150,150,150,150,150,pi,pi,pi,pithe upper bounds for the gridGRID_SPACING=0.1,0.1,0.01,0.1,0.1,0.01,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.01,0.01,0.01,0.01the approximate grid spacing (to be used as an alternative or together with GRID_BIN)GRID_WSTRIDE=10000 #GRID_RFILES=GRID.helix.lessthan,GRID.beta,GRID.rgyr,GRID.hydro,GRID.salt,GRID.dihcor,GRID.reg1,GRID.reg2,GRID.reg3,GRID.reg4,GRID.reg5,GRID.reg6,GRID.reg7,GRID.reg8,GRID.reg9,GRID.reg10,GRID.reg11,GRID.reg12,GRID.reg13,GRID.reg14,GRID.ligtor1,GRID.ligtor2,GRID.ligtor3,GRID.ligtor4frequency for dumping the gridFILE=HILLS_helix,HILLS_beta,HILLS_rgyr,HILLS_hydro,HILLS_salt,HILLS_dihcor,HILLS_reg1,HILLS_reg2,HILLS_reg3,HILLS_reg4,HILLS_reg5,HILLS_reg6,HILLS_reg7,HILLS_reg8,HILLS_reg9,HILLS_reg10,HILLS_reg11,HILLS_reg12,HILLS_reg13,HILLS_reg14,HILLS_ligtor1,HILLS_ligtor2,HILLS_ligtor3,HILLS_ligtor4files in which the lists of added hills are stored, default names are assigned using arguments if FILE is not foundWALKERS_MPISwitch on MPI version of multiple walkers - not compatible with WALKERS_* options other than WALKERS_DIRLABEL=pbmetad ... PBMETADa label for the action so that its output can be referenced in the input to other actions
# Metainference - one sigma per nucleus 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 derivativesSIGMA0=9.0initial value of the uncertainty parameterSIGMA_MIN=0.00001minimum value of the uncertainty parameterSIGMA_MAX=10.0maximum value of the uncertainty parameterDSIGMA=0.1maximum MC move of the uncertainty parameterNOISETYPE=GAUSSfunctional form of the noise (GAUSS,MGAUSS,OUTLIERS,MOUTLIERS,GENERIC)REWEIGHTsimple REWEIGHT using the latest ARG as energySIGMA_MEAN0=0.5starting value for the uncertainty in the mean estimateOPTSIGMAMEAN=SEMSet to NONE/SEM to manually set sigma mean, or to estimate it on the flyAVERAGING=500Stride for calculation of averaged weights and sigma_meanWRITE_STRIDE=2500write the status to a file every N steps, this can be used for restart/continuationSTATUS_FILE=MISTATUS.cs_ha cs_hn:write a file with all the data useful for restart/continuation of MetainferenceMETAINFERENCECalculates 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 derivativesSIGMA0=9.0initial value of the uncertainty parameterSIGMA_MIN=0.00001minimum value of the uncertainty parameterSIGMA_MAX=10.0maximum value of the uncertainty parameterDSIGMA=0.1maximum MC move of the uncertainty parameterNOISETYPE=GAUSSfunctional form of the noise (GAUSS,MGAUSS,OUTLIERS,MOUTLIERS,GENERIC)REWEIGHTsimple REWEIGHT using the latest ARG as energySIGMA_MEAN0=0.5starting value for the uncertainty in the mean estimateOPTSIGMAMEAN=SEMSet to NONE/SEM to manually set sigma mean, or to estimate it on the flyAVERAGING=500Stride for calculation of averaged weights and sigma_meanWRITE_STRIDE=2500write the status to a file every N steps, this can be used for restart/continuationSTATUS_FILE=MISTATUS.cs_hn cs_nh:write a file with all the data useful for restart/continuation of MetainferenceMETAINFERENCECalculates the Metainference energy for a set of experimental data. More detailsARG=(cs\.nh-.*),pbmetad.biasthe input for this action is the scalar output from one or more other actionsPARARG=(cs\.expnhreference values for the experimental data, these can be provided as arguments without derivativesSIGMA0=9.0initial value of the uncertainty parameterSIGMA_MIN=0.00001minimum value of the uncertainty parameterSIGMA_MAX=10.0maximum value of the uncertainty parameterDSIGMA=0.1maximum MC move of the uncertainty parameterNOISETYPE=GAUSSfunctional form of the noise (GAUSS,MGAUSS,OUTLIERS,MOUTLIERS,GENERIC)REWEIGHTsimple REWEIGHT using the latest ARG as energySIGMA_MEAN0=0.5starting value for the uncertainty in the mean estimateOPTSIGMAMEAN=SEMSet to NONE/SEM to manually set sigma mean, or to estimate it on the flyAVERAGING=500Stride for calculation of averaged weights and sigma_meanWRITE_STRIDE=2500write the status to a file every N steps, this can be used for restart/continuationSTATUS_FILE=MISTATUS.cs_nh cs_ca:write a file with all the data useful for restart/continuation of MetainferenceMETAINFERENCECalculates 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 derivativesSIGMA0=9.0initial value of the uncertainty parameterSIGMA_MIN=0.00001minimum value of the uncertainty parameterSIGMA_MAX=10.0maximum value of the uncertainty parameterDSIGMA=0.1maximum MC move of the uncertainty parameterNOISETYPE=GAUSSfunctional form of the noise (GAUSS,MGAUSS,OUTLIERS,MOUTLIERS,GENERIC)REWEIGHTsimple REWEIGHT using the latest ARG as energySIGMA_MEAN0=0.5starting value for the uncertainty in the mean estimateOPTSIGMAMEAN=SEMSet to NONE/SEM to manually set sigma mean, or to estimate it on the flyAVERAGING=500Stride for calculation of averaged weights and sigma_meanWRITE_STRIDE=2500write the status to a file every N steps, this can be used for restart/continuationSTATUS_FILE=MISTATUS.cs_ca cs_cb:write a file with all the data useful for restart/continuation of MetainferenceMETAINFERENCECalculates 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 derivativesSIGMA0=9.0initial value of the uncertainty parameterSIGMA_MIN=0.00001minimum value of the uncertainty parameterSIGMA_MAX=10.0maximum value of the uncertainty parameterDSIGMA=0.1maximum MC move of the uncertainty parameterNOISETYPE=GAUSSfunctional form of the noise (GAUSS,MGAUSS,OUTLIERS,MOUTLIERS,GENERIC)REWEIGHTsimple REWEIGHT using the latest ARG as energySIGMA_MEAN0=0.5starting value for the uncertainty in the mean estimateOPTSIGMAMEAN=SEMSet to NONE/SEM to manually set sigma mean, or to estimate it on the flyAVERAGING=500Stride for calculation of averaged weights and sigma_meanWRITE_STRIDE=2500write the status to a file every N steps, this can be used for restart/continuationSTATUS_FILE=MISTATUS.cs_cb cs_co:write a file with all the data useful for restart/continuation of MetainferenceMETAINFERENCECalculates the Metainference energy for a set of experimental data. More detailsARG=(cs\.co-.*),pbmetad.biasthe input for this action is the scalar output from one or more other actionsPARARG=(cs\.expcoreference values for the experimental data, these can be provided as arguments without derivativesSIGMA0=9.0initial value of the uncertainty parameterSIGMA_MIN=0.00001minimum value of the uncertainty parameterSIGMA_MAX=10.0maximum value of the uncertainty parameterDSIGMA=0.1maximum MC move of the uncertainty parameterNOISETYPE=GAUSSfunctional form of the noise (GAUSS,MGAUSS,OUTLIERS,MOUTLIERS,GENERIC)REWEIGHTsimple REWEIGHT using the latest ARG as energySIGMA_MEAN0=0.5starting value for the uncertainty in the mean estimateOPTSIGMAMEAN=SEMSet to NONE/SEM to manually set sigma mean, or to estimate it on the flyAVERAGING=500Stride for calculation of averaged weights and sigma_meanWRITE_STRIDE=2500write the status to a file every N steps, this can be used for restart/continuationSTATUS_FILE=MISTATUS.cs_cowrite a file with all the data useful for restart/continuation of Metainference
# Ensemble statistics ens:ENSEMBLECalculates the replica averaging of a collective variable over multiple replicas. More detailsARG=(cs\.ha-.*),(cs\.hn-.*),(cs\.nh-.*),(cs\.ca-.*),(cs\.cb-.*),(cs\.co-.*),pbmetad.biasthe input for this action is the scalar output from one or more other actionsREWEIGHTsimple REWEIGHT using the latest ARG as energySTATS...Calculates statistical properties of a set of collective variables with respect to a set of reference values. More detailsARG=(ens\.cs\.ha-.*),(ens\.cs\.hn-.*),(ens\.cs\.nh-.*),(ens\.cs\.ca-.*),(ens\.cs\.cb-.*),(ens\.cs\.cothe input for this action is the scalar output from one or more other actionsPARARG=(cs\.expha-.*),(cs\.exphn-.*),(cs\.expnh-.*),(cs\.expca-.*),(cs\.expcb-.*),(cs\.expcothe input for this action is the scalar output from one or more other actions without derivativesLABEL=stat ... STATSa label for the action so that its output can be referenced in the input to other actionsPrint quantities to a file. More detailsARG=helix.lessthan,beta,rgyr,hydro,salt,dihcor,reg1,reg2,reg3,reg4,reg5,reg6,reg7,reg8,reg9,reg10,reg11,reg12,reg13,reg14,ligtor1,ligtor2,ligtor3,ligtor4,pbmetad.biasthe input for this action is the scalar output from one or more other actionsFILE=COLVARthe name of the file on which to output these quantitiesSTRIDE=500the frequency with which the quantities of interest should be outputPrint quantities to a file. More detailsARG=(ens.*),(statthe input for this action is the scalar output from one or more other actionsFILE=STATSthe name of the file on which to output these quantitiesSTRIDE=500the frequency with which the quantities of interest should be outputPrint quantities to a file. More detailsARG=(cs_hathe input for this action is the scalar output from one or more other actionsFILE=BAYES.HAthe name of the file on which to output these quantitiesSTRIDE=500the frequency with which the quantities of interest should be outputPrint quantities to a file. More detailsARG=(cs_hnthe input for this action is the scalar output from one or more other actionsFILE=BAYES.HNthe name of the file on which to output these quantitiesSTRIDE=500the frequency with which the quantities of interest should be outputPrint quantities to a file. More detailsARG=(cs_nhthe input for this action is the scalar output from one or more other actionsFILE=BAYES.NHthe name of the file on which to output these quantitiesSTRIDE=500the frequency with which the quantities of interest should be outputPrint quantities to a file. More detailsARG=(cs_cathe input for this action is the scalar output from one or more other actionsFILE=BAYES.CAthe name of the file on which to output these quantitiesSTRIDE=500the frequency with which the quantities of interest should be outputPrint quantities to a file. More detailsARG=(cs_cbthe input for this action is the scalar output from one or more other actionsFILE=BAYES.CBthe name of the file on which to output these quantitiesSTRIDE=500the frequency with which the quantities of interest should be outputPrint quantities to a file. More detailsARG=(cs_cothe input for this action is the scalar output from one or more other actionsFILE=BAYES.COthe name of the file on which to output these quantitiesSTRIDE=500the frequency with which the quantities of interest should be outputENDPLUMEDTerminate plumed input. More details