Project ID: plumID:23.005
Source: apo-5HT1A/plumed_reweight_microsw_5ht1a_rec.dat
Originally used with PLUMED version: 2.5.3
Stable: zipped raw stdout - zipped raw stderr - stderr
Master: zipped raw stdout - zipped raw stderr - stderr
## Rebuild molecules that can become split by PBC # #MOLINFO STRUCTURE=5ht1a_rec_ref.pdb #WHOLEMOLECULES STRIDE=1 ENTITY0=1-4932
rbiasREADRead quantities from a colvar file. This action has hidden defaults. More detailsFILE=COLVARthe name of the file from which to read these quantitiesVALUES=meta.rbiasthe values to read from the fileIGNORE_TIME: tm3-tm6_1ignore the time in the colvar fileREADRead quantities from a colvar file. This action has hidden defaults. More detailsFILE=COLVARthe name of the file from which to read these quantitiesVALUES=tm3-tm6_1the values to read from the fileIGNORE_TIME: NPxxYignore the time in the colvar fileREADRead quantities from a colvar file. This action has hidden defaults. More detailsFILE=COLVARthe name of the file from which to read these quantitiesVALUES=NPxxYthe values to read from the fileIGNORE_TIME: yyignore the time in the colvar fileREADRead quantities from a colvar file. This action has hidden defaults. More detailsFILE=COLVARthe name of the file from which to read these quantitiesVALUES=yythe values to read from the fileIGNORE_TIME: PIF_aignore the time in the colvar fileREADRead quantities from a colvar file. This action has hidden defaults. More detailsFILE=COLVARthe name of the file from which to read these quantitiesVALUES=PIF_athe values to read from the fileIGNORE_TIME:ignore the time in the colvar file
biasREWEIGHT_METADCalculate the weights configurations should contribute to the histogram in a simulation in which a metadynamics bias acts upon the system. This action has hidden defaults. More detailsTEMP=310 :the system temperatureHISTOGRAM...Accumulate the average probability density along a few CVs from a trajectory. This action is a shortcut and it has hidden defaults. More detailsARG=tm3-tm6_1the quantity that is being averagedBANDWIDTH=0.006the bandwidths for kernel density esimtationLOGWEIGHTS=biasthe logarithm of the quantity to use as the weights when calculating averagesLABEL=histo5a label for the action so that its output can be referenced in the input to other actionsGRID_MIN=0.55the lower bounds for the gridGRID_MAX=1.97the upper bounds for the gridGRID_BIN=150 ...the number of bins for the gridHISTOGRAM...Accumulate the average probability density along a few CVs from a trajectory. This action is a shortcut and it has hidden defaults. More detailsARG=NPxxYthe quantity that is being averagedBANDWIDTH=0.006the bandwidths for kernel density esimtationLOGWEIGHTS=biasthe logarithm of the quantity to use as the weights when calculating averagesLABEL=histo6a label for the action so that its output can be referenced in the input to other actionsGRID_MIN=0.052the lower bounds for the gridGRID_MAX=0.88the upper bounds for the gridGRID_BIN=150 ...the number of bins for the gridHISTOGRAM...Accumulate the average probability density along a few CVs from a trajectory. This action is a shortcut and it has hidden defaults. More detailsARG=PIF_athe quantity that is being averagedBANDWIDTH=0.01the bandwidths for kernel density esimtationLOGWEIGHTS=biasthe logarithm of the quantity to use as the weights when calculating averagesLABEL=histo7a label for the action so that its output can be referenced in the input to other actionsGRID_MIN=0.0the lower bounds for the gridGRID_MAX=0.656the upper bounds for the gridGRID_BIN=150 ...the number of bins for the gridHISTOGRAM...Accumulate the average probability density along a few CVs from a trajectory. This action is a shortcut and it has hidden defaults. More detailsARG=yythe quantity that is being averagedBANDWIDTH=0.035the bandwidths for kernel density esimtationLOGWEIGHTS=biasthe logarithm of the quantity to use as the weights when calculating averagesLABEL=histo9a label for the action so that its output can be referenced in the input to other actionsGRID_MIN=0.30the lower bounds for the gridGRID_MAX=2.10the upper bounds for the gridGRID_BIN=150 ...the number of bins for the grid
ff5CONVERT_TO_FESConvert a histogram to a free energy surface. This action is a shortcut. More detailsGRID=histo5the histogram that you would like to convert into a free energy surface (old syntax)TEMP=310 :the temperature at which you are operatingDUMPGRIDOutput the function on the grid to a file with the PLUMED grid format. More detailsGRID=ff5the grid you would like to print (can also use ARG for specifying what is being printed)FILE=mw_fes_5ht1a_rec_tm3-tm6_1.datthe file on which to write the grid
ff6CONVERT_TO_FESConvert a histogram to a free energy surface. This action is a shortcut. More detailsGRID=histo6the histogram that you would like to convert into a free energy surface (old syntax)TEMP=310 :the temperature at which you are operatingDUMPGRIDOutput the function on the grid to a file with the PLUMED grid format. More detailsGRID=ff6the grid you would like to print (can also use ARG for specifying what is being printed)FILE=mw_fes_5ht1a_rec_NPxxY.datthe file on which to write the grid
ff7CONVERT_TO_FESConvert a histogram to a free energy surface. This action is a shortcut. More detailsGRID=histo7the histogram that you would like to convert into a free energy surface (old syntax)TEMP=310 :the temperature at which you are operatingDUMPGRIDOutput the function on the grid to a file with the PLUMED grid format. More detailsGRID=ff7the grid you would like to print (can also use ARG for specifying what is being printed)FILE=mw_fes_5ht1a_rec_PIF_a.datthe file on which to write the grid
ff9CONVERT_TO_FESConvert a histogram to a free energy surface. This action is a shortcut. More detailsGRID=histo9the histogram that you would like to convert into a free energy surface (old syntax)TEMP=310 :the temperature at which you are operatingDUMPGRIDOutput the function on the grid to a file with the PLUMED grid format. More detailsGRID=ff9the grid you would like to print (can also use ARG for specifying what is being printed)FILE=mw_fes_5ht1a_rec_yy.datthe file on which to write the grid