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

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 metadynamic metainference simulations

# define groups 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 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=1-627 FLUSHThis command instructs plumed to flush all the open files with a user specified frequency. More details STRIDEthe frequency with which all the open files should be flushed=1000 #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=CVs.dat
# Chemical shifts at 278 K cs: CS2BACKBONECalculates the backbone chemical shifts for a protein. This action has hidden defaults. More details ATOMSThe atoms to be included in the calculation, e=1-627 DATADIR The folder with the experimental chemical shifts=../data NOPBC ignore the periodic boundary conditions when calculating distances TEMPLATE A PDB file of the protein system=../system/template.pdb
#activate parallel bias metadynamics PBMETADUsed to performed Parallel Bias metadynamics. More details ... ARGthe labels of the scalars on which the bias will act=helix.lessthan,beta,rgyr,hydro,salt,dihcor HEIGHTthe height of the Gaussian hills, one for all biases=1.2 BIASFACTORuse well tempered metadynamics with this bias factor, one for all biases=24 #10*SQRT(NUM_OF_CVS) SIGMAthe widths of the Gaussian hills=0.64,0.33,0.03,0.69,2.75,1.34 PACEthe frequency for hill addition, one for all biases=500 GRID_MINthe lower bounds for the grid=-1,-1,-1,-1,-1,-1 GRID_MAXthe upper bounds for the grid=100,100,20,200,400,50 GRID_SPACINGthe approximate grid spacing (to be used as an alternative or together with GRID_BIN)=0.1,0.1,0.01,0.1,0.1,0.01 GRID_WSTRIDEfrequency for dumping the grid=10000 # GRID_RFILES=GRID.helix.lessthan,GRID.beta,GRID.rgyr,GRID.hydro,GRID.salt,GRID.dihcor FILEfiles in which the lists of added hills are stored, default names are assigned using arguments if FILE is not found=HILLS_helix,HILLS_beta,HILLS_rgyr,HILLS_hydro,HILLS_salt,HILLS_dihcor WALKERS_MPI Switch on MPI version of multiple walkers - not compatible with WALKERS_* options other than WALKERS_DIR LABELa label for the action so that its output can be referenced in the input to other actions=pbmetad ... PBMETAD
# Metainference - one sigma per nucleus 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-.*) SIGMA0 initial value of the uncertainty parameter=9.0 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=0.1 NOISETYPE functional form of the noise (GAUSS,MGAUSS,OUTLIERS,MOUTLIERS,GENERIC)=GAUSS REWEIGHT simple REWEIGHT using the latest ARG as energy SIGMA_MEAN0starting value for the uncertainty in the mean estimate=0.5 OPTSIGMAMEAN Set to NONE/SEM to manually set sigma mean, or to estimate it on the fly=SEM AVERAGINGStride for calculation of averaged weights and sigma_mean=500 WRITE_STRIDE write the status to a file every N steps, this can be used for restart/continuation=2500 STATUS_FILEwrite a file with all the data useful for restart/continuation of Metainference=MISTATUS.cs_ha 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-.*) SIGMA0 initial value of the uncertainty parameter=9.0 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=0.1 NOISETYPE functional form of the noise (GAUSS,MGAUSS,OUTLIERS,MOUTLIERS,GENERIC)=GAUSS REWEIGHT simple REWEIGHT using the latest ARG as energy SIGMA_MEAN0starting value for the uncertainty in the mean estimate=0.5 OPTSIGMAMEAN Set to NONE/SEM to manually set sigma mean, or to estimate it on the fly=SEM AVERAGINGStride for calculation of averaged weights and sigma_mean=500 WRITE_STRIDE write the status to a file every N steps, this can be used for restart/continuation=2500 STATUS_FILEwrite a file with all the data useful for restart/continuation of Metainference=MISTATUS.cs_hn cs_nh: METAINFERENCECalculates the Metainference energy for a set of experimental data. More details ARGthe labels of the scalars on which the bias will act=(cs\.nh-.*),pbmetad.bias PARARGreference values for the experimental data, these can be provided as arguments without derivatives=(cs\.expnh-.*) SIGMA0 initial value of the uncertainty parameter=9.0 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=0.1 NOISETYPE functional form of the noise (GAUSS,MGAUSS,OUTLIERS,MOUTLIERS,GENERIC)=GAUSS REWEIGHT simple REWEIGHT using the latest ARG as energy SIGMA_MEAN0starting value for the uncertainty in the mean estimate=0.5 OPTSIGMAMEAN Set to NONE/SEM to manually set sigma mean, or to estimate it on the fly=SEM AVERAGINGStride for calculation of averaged weights and sigma_mean=500 WRITE_STRIDE write the status to a file every N steps, this can be used for restart/continuation=2500 STATUS_FILEwrite a file with all the data useful for restart/continuation of Metainference=MISTATUS.cs_nh 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-.*) SIGMA0 initial value of the uncertainty parameter=9.0 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=0.1 NOISETYPE functional form of the noise (GAUSS,MGAUSS,OUTLIERS,MOUTLIERS,GENERIC)=GAUSS REWEIGHT simple REWEIGHT using the latest ARG as energy SIGMA_MEAN0starting value for the uncertainty in the mean estimate=0.5 OPTSIGMAMEAN Set to NONE/SEM to manually set sigma mean, or to estimate it on the fly=SEM AVERAGINGStride for calculation of averaged weights and sigma_mean=500 WRITE_STRIDE write the status to a file every N steps, this can be used for restart/continuation=2500 STATUS_FILEwrite a file with all the data useful for restart/continuation of Metainference=MISTATUS.cs_ca 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-.*) SIGMA0 initial value of the uncertainty parameter=9.0 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=0.1 NOISETYPE functional form of the noise (GAUSS,MGAUSS,OUTLIERS,MOUTLIERS,GENERIC)=GAUSS REWEIGHT simple REWEIGHT using the latest ARG as energy SIGMA_MEAN0starting value for the uncertainty in the mean estimate=0.5 OPTSIGMAMEAN Set to NONE/SEM to manually set sigma mean, or to estimate it on the fly=SEM AVERAGINGStride for calculation of averaged weights and sigma_mean=500 WRITE_STRIDE write the status to a file every N steps, this can be used for restart/continuation=2500 STATUS_FILEwrite a file with all the data useful for restart/continuation of Metainference=MISTATUS.cs_cb cs_co: METAINFERENCECalculates the Metainference energy for a set of experimental data. More details ARGthe labels of the scalars on which the bias will act=(cs\.co-.*),pbmetad.bias PARARGreference values for the experimental data, these can be provided as arguments without derivatives=(cs\.expco-.*) SIGMA0 initial value of the uncertainty parameter=9.0 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=0.1 NOISETYPE functional form of the noise (GAUSS,MGAUSS,OUTLIERS,MOUTLIERS,GENERIC)=GAUSS REWEIGHT simple REWEIGHT using the latest ARG as energy SIGMA_MEAN0starting value for the uncertainty in the mean estimate=0.5 OPTSIGMAMEAN Set to NONE/SEM to manually set sigma mean, or to estimate it on the fly=SEM AVERAGINGStride for calculation of averaged weights and sigma_mean=500 WRITE_STRIDE write the status to a file every N steps, this can be used for restart/continuation=2500 STATUS_FILEwrite a file with all the data useful for restart/continuation of Metainference=MISTATUS.cs_co # Ensemble statistics ens: ENSEMBLECalculates the replica averaging of a collective variable over multiple replicas. More details ARGthe labels of the values from which the function is calculated=(cs\.ha-.*),(cs\.hn-.*),(cs\.nh-.*),(cs\.ca-.*),(cs\.cb-.*),(cs\.co-.*),pbmetad.bias REWEIGHT simple REWEIGHT using the latest ARG as energy
STATSCalculates statistical properties of a set of collective variables with respect to a set of reference values. More details ... ARGthe labels of the values from which the function is calculated=(ens\.cs\.ha-.*),(ens\.cs\.hn-.*),(ens\.cs\.nh-.*),(ens\.cs\.ca-.*),(ens\.cs\.cb-.*),(ens\.cs\.co-.*) PARARGthe input for this action is the scalar output from one or more other actions without derivatives=(cs\.expha-.*),(cs\.exphn-.*),(cs\.expnh-.*),(cs\.expca-.*),(cs\.expcb-.*),(cs\.expco-.*) LABELa label for the action so that its output can be referenced in the input to other actions=stat ... STATS
#print out relevant info PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=helix.lessthan,beta,rgyr,hydro,salt,dihcor,pbmetad.bias FILEthe name of the file on which to output these quantities=COLVAR STRIDE the frequency with which the quantities of interest should be output=500 PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=(ens.*),(stat.*) FILEthe name of the file on which to output these quantities=STATS STRIDE the frequency with which the quantities of interest should be output=500 PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=(cs_ha.*) FILEthe name of the file on which to output these quantities=BAYES.HA STRIDE the frequency with which the quantities of interest should be output=500 PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=(cs_hn.*) FILEthe name of the file on which to output these quantities=BAYES.HN STRIDE the frequency with which the quantities of interest should be output=500 PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=(cs_nh.*) FILEthe name of the file on which to output these quantities=BAYES.NH STRIDE the frequency with which the quantities of interest should be output=500 PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=(cs_ca.*) FILEthe name of the file on which to output these quantities=BAYES.CA STRIDE the frequency with which the quantities of interest should be output=500 PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=(cs_cb.*) FILEthe name of the file on which to output these quantities=BAYES.CB STRIDE the frequency with which the quantities of interest should be output=500 PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=(cs_co.*) FILEthe name of the file on which to output these quantities=BAYES.CO STRIDE the frequency with which the quantities of interest should be output=500 ENDPLUMEDTerminate plumed input. More details