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
Click on the labels of the actions for more information on what each action computes
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## 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 input for this action is the scalar output from one or more other actionsBANDWIDTH=0.006,0.035the bandwidths for kernel density estimationLOGWEIGHTS=biaslist of actions that calculates log weights that should be used to weight configurations 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 input for this action is the scalar output from one or more other actionsBANDWIDTH=0.006,0.006the bandwidths for kernel density estimationLOGWEIGHTS=biaslist of actions that calculates log weights that should be used to weight configurations 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 input for this action is the scalar output from one or more other actionsBANDWIDTH=0.006,0.01the bandwidths for kernel density estimationLOGWEIGHTS=biaslist of actions that calculates log weights that should be used to weight configurations 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, H(x), to a free energy surface using F(x) = -k_B T ln H(x). More detailsGRID=histo1the action that creates the input grid you would like to useTEMP=310the temperature at which you are operatingDUMPGRIDOutput the function on the grid to a file with the PLUMED grid format. More detailsGRID=ff1the action that creates the grid you would like to outputFILE=mw_fes_5ht1a_rec_tm3-tm6_yy.datthe file on which to write the grid
ff2:CONVERT_TO_FESConvert a histogram, H(x), to a free energy surface using F(x) = -k_B T ln H(x). More detailsGRID=histo2the action that creates the input grid you would like to useTEMP=310the temperature at which you are operatingDUMPGRIDOutput the function on the grid to a file with the PLUMED grid format. More detailsGRID=ff2the action that creates the grid you would like to outputFILE=mw_fes_5ht1a_rec_tm3-tm6_NPxxY.datthe file on which to write the grid
ff3:CONVERT_TO_FESConvert a histogram, H(x), to a free energy surface using F(x) = -k_B T ln H(x). More detailsGRID=histo3the action that creates the input grid you would like to useTEMP=310the temperature at which you are operatingDUMPGRIDOutput the function on the grid to a file with the PLUMED grid format. More detailsGRID=ff3the action that creates the grid you would like to outputFILE=mw_fes_5ht1a_rec_tm3-tm6_PIF.datthe file on which to write the grid