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

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 ENTITY1the atoms that make up a molecule that you wish to align=628-664
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 on peptide
INCLUDEIncludes an external input file, similar to #include in C preprocessor. More details. Show included file FILEfile to be included=CVs.dat

#include file with definition of metadynamics CVs involving the small molecule
INCLUDEIncludes an external input file, similar to #include in C preprocessor. More details. Show included file FILEfile to be included=CVs_drug.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,reg1,reg2,reg3,reg4,reg5,reg6,reg7,reg8,reg9,reg10,reg11,reg12,reg13,reg14,ligtor1,ligtor2,ligtor3,ligtor4
    HEIGHTthe height of the Gaussian hills, one for all biases=1.2
    BIASFACTORuse well tempered metadynamics with this bias factor, one for all biases=49 #10*SQRT(NUM_OF_CVS)
    SIGMAthe widths of the Gaussian hills=0.64,0.33,0.03,0.69,2.75,1.34,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,0.1,0.1,0.1,0.1
    PACEthe frequency for hill addition, one for all biases=500
    GRID_MINthe lower bounds for the grid=-1,-1,-1,-1,-1,-1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,-pi,-pi,-pi,-pi
    GRID_MAXthe upper bounds for the grid=100,100,20,200,400,50,150,150,150,150,150,150,150,150,150,150,150,150,150,150,pi,pi,pi,pi
    GRID_SPACINGthe approximate grid spacing (to be used as an alternative or together with GRID_BIN)=0.1,0.1,0.01,0.1,0.1,0.01,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.01,0.01,0.01,0.01    
    GRID_WSTRIDEfrequency for dumping the grid=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.ligtor4
    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,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_ligtor4
    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

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,reg1,reg2,reg3,reg4,reg5,reg6,reg7,reg8,reg9,reg10,reg11,reg12,reg13,reg14,ligtor1,ligtor2,ligtor3,ligtor4,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