Project ID: plumID:23.005
Source: apo-5HT1A/plumed_reweight_2D_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
rbias:READRead quantities from a colvar file. More detailsFILE=COLVARthe name of the file from which to read these quantitiesVALUES=meta.rbiasthe values to read from the fileIGNORE_TIMEtm3-tm6_1:ignore the time in the colvar fileREADRead quantities from a colvar file. More detailsFILE=COLVARthe name of the file from which to read these quantitiesVALUES=tm3-tm6_1the values to read from the fileIGNORE_TIMENPxxY:ignore the time in the colvar fileREADRead quantities from a colvar file. More detailsFILE=COLVARthe name of the file from which to read these quantitiesVALUES=NPxxYthe values to read from the fileIGNORE_TIMEyy:ignore the time in the colvar fileREADRead quantities from a colvar file. More detailsFILE=COLVARthe name of the file from which to read these quantitiesVALUES=yythe values to read from the fileIGNORE_TIMEPIF_a:ignore the time in the colvar fileREADRead quantities from a colvar file. More detailsFILE=COLVARthe name of the file from which to read these quantitiesVALUES=PIF_athe values to read from the fileIGNORE_TIMEignore the time in the colvar file
bias:REWEIGHT_METADCalculate the weights configurations should contribute to the histogram in a simulation in which a metadynamics bias acts upon the system. More detailsTEMP=310the system temperatureHISTOGRAM...Accumulate the average probability density along a few CVs from a trajectory. More detailsARG=tm3-tm6_1,yythe quantities that are being used to construct the histogramBANDWIDTH=0.006,0.035the bandwidths for kernel density esimtationLOGWEIGHTS=biasthe logarithm of the quantity to use as the weights when calculating averagesLABEL=histo1a label for the action so that its output can be referenced in the input to other actionsGRID_MIN=0.5,0.2the lower bounds for the gridGRID_MAX=2.0,2.2the upper bounds for the gridGRID_BIN=150,150 ...the number of bins for the gridHISTOGRAM...Accumulate the average probability density along a few CVs from a trajectory. More detailsARG=tm3-tm6_1,NPxxYthe quantities that are being used to construct the histogramBANDWIDTH=0.006,0.006the bandwidths for kernel density esimtationLOGWEIGHTS=biasthe logarithm of the quantity to use as the weights when calculating averagesLABEL=histo2a label for the action so that its output can be referenced in the input to other actionsGRID_MIN=0.5,0.0the lower bounds for the gridGRID_MAX=2.0,0.9the upper bounds for the gridGRID_BIN=150,150 ...the number of bins for the gridHISTOGRAM...Accumulate the average probability density along a few CVs from a trajectory. More detailsARG=tm3-tm6_1,PIF_athe quantities that are being used to construct the histogramBANDWIDTH=0.006,0.01the bandwidths for kernel density esimtationLOGWEIGHTS=biasthe logarithm of the quantity to use as the weights when calculating averagesLABEL=histo3a label for the action so that its output can be referenced in the input to other actionsGRID_MIN=0.5,-0.05the lower bounds for the gridGRID_MAX=2.0,0.7the upper bounds for the gridGRID_BIN=150,150 ...the number of bins for the grid
ff1:CONVERT_TO_FESConvert a histogram to a free energy surface. More detailsGRID=histo1the histogram that you would like to convert into a free energy surface (old syntax)TEMP=310the temperature at which you are operatingDUMPGRIDOutput the function on the grid to a file with the PLUMED grid format. More detailsGRID=ff1the grid you would like to print (can also use ARG for specifying what is being printed)FILE=mw_fes_5ht1a_rec_tm3-tm6_yy.datthe file on which to write the grid
ff2:CONVERT_TO_FESConvert a histogram to a free energy surface. More detailsGRID=histo2the histogram that you would like to convert into a free energy surface (old syntax)TEMP=310the temperature at which you are operatingDUMPGRIDOutput the function on the grid to a file with the PLUMED grid format. More detailsGRID=ff2the grid you would like to print (can also use ARG for specifying what is being printed)FILE=mw_fes_5ht1a_rec_tm3-tm6_NPxxY.datthe file on which to write the grid
ff3:CONVERT_TO_FESConvert a histogram to a free energy surface. More detailsGRID=histo3the histogram that you would like to convert into a free energy surface (old syntax)TEMP=310the temperature at which you are operatingDUMPGRIDOutput the function on the grid to a file with the PLUMED grid format. More detailsGRID=ff3the grid you would like to print (can also use ARG for specifying what is being printed)FILE=mw_fes_5ht1a_rec_tm3-tm6_PIF.datthe file on which to write the grid