**Project ID:** plumID:20.014

**Source:** PLUMED_input_files/AB42_alone/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 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 CVsINCLUDEIncludes an external input file, similar to #include in C preprocessor. More details. Show included fileFILE=CVs.datfile to be included

# Chemical shifts at 278 Kcs:CS2BACKBONECalculates the backbone chemical shifts for a protein. This action has hidden defaults. More detailsATOMS=1-627The atoms to be included in the calculation, eDATADIR=The folder with the experimental chemical shifts../dataNOPBCignore the periodic boundary conditions when calculating distancesTEMPLATE=A PDB file of the protein system../system/template.pdb

#activate parallel bias metadynamicsPBMETAD...Used to performed Parallel Bias metadynamics. More detailsARG=the input for this action is the scalar output from one or more other actionshelix.lessthan,beta,rgyr,hydro,salt,dihcorHEIGHT=1.2the height of the Gaussian hills, one for all biasesBIASFACTOR=24 #10*SQRT(NUM_OF_CVS)use well tempered metadynamics with this bias factor, one for all biasesSIGMA=0.64,0.33,0.03,0.69,2.75,1.34the widths of the Gaussian hillsPACE=500the frequency for hill addition, one for all biasesGRID_MIN=-1,-1,-1,-1,-1,-1the lower bounds for the gridGRID_MAX=100,100,20,200,400,50the upper bounds for the gridGRID_SPACING=0.1,0.1,0.01,0.1,0.1,0.01the 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.dihcorfrequency for dumping the gridFILE=HILLS_helix,HILLS_beta,HILLS_rgyr,HILLS_hydro,HILLS_salt,HILLS_dihcorfiles 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=a label for the action so that its output can be referenced in the input to other actionspbmetad... PBMETAD

# Metainference - one sigma per nucleuscs_ha:METAINFERENCECalculates the Metainference energy for a set of experimental data. More detailsARG=(cs\.ha-.*),the input for this action is the scalar output from one or more other actionspbmetad.biasPARARG=(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_hawrite a file with all the data useful for restart/continuation of Metainferencecs_hn:METAINFERENCECalculates the Metainference energy for a set of experimental data. More detailsARG=(cs\.hn-.*),the input for this action is the scalar output from one or more other actionspbmetad.biasPARARG=(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_hnwrite a file with all the data useful for restart/continuation of Metainferencecs_nh:METAINFERENCECalculates the Metainference energy for a set of experimental data. More detailsARG=(cs\.nh-.*),the input for this action is the scalar output from one or more other actionspbmetad.biasPARARG=(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_nhwrite a file with all the data useful for restart/continuation of Metainferencecs_ca:METAINFERENCECalculates the Metainference energy for a set of experimental data. More detailsARG=(cs\.ca-.*),the input for this action is the scalar output from one or more other actionspbmetad.biasreference 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_cawrite a file with all the data useful for restart/continuation of Metainferencecs_cb:METAINFERENCECalculates the Metainference energy for a set of experimental data. More detailsARG=(cs\.cb-.*),the input for this action is the scalar output from one or more other actionspbmetad.biasreference 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_cbwrite a file with all the data useful for restart/continuation of Metainferencecs_co:METAINFERENCECalculates the Metainference energy for a set of experimental data. More detailsARG=(cs\.co-.*),the input for this action is the scalar output from one or more other actionspbmetad.biasreference 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 statisticsens: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-.*),the input for this action is the scalar output from one or more other actionspbmetad.biasREWEIGHTsimple 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=a label for the action so that its output can be referenced in the input to other actionsstat... STATS

#print out relevant infoPrint quantities to a file. More detailsARG=the input for this action is the scalar output from one or more other actionshelix.lessthan,beta,rgyr,hydro,salt,dihcor,pbmetad.biasFILE=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