**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=1-4932rbias: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_TIMEignore the time in the colvar filetm3-tm6_1:READRead quantities from a colvar file. More detailsFILE=COLVARthe name of the file from which to read these quantitiesVALUES=the values to read from the filetm3-tm6_1IGNORE_TIMEignore the time in the colvar fileNPxxY:READRead quantities from a colvar file. More detailsFILE=COLVARthe name of the file from which to read these quantitiesVALUES=the values to read from the fileNPxxYIGNORE_TIMEignore the time in the colvar fileyy:READRead quantities from a colvar file. More detailsFILE=COLVARthe name of the file from which to read these quantitiesVALUES=the values to read from the fileyyIGNORE_TIMEignore the time in the colvar filePIF_a:READRead quantities from a colvar file. More detailsFILE=COLVARthe name of the file from which to read these quantitiesVALUES=the values to read from the filePIF_aIGNORE_TIMEignore the time in the colvar filebias: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=the input for this action is the scalar output from one or more other actionstm3-tm6_1BANDWIDTH=0.006the bandwidths for kernel density estimationLOGWEIGHTS=list of actions that calculates log weights that should be used to weight configurations when calculating averagesbiasLABEL=a label for the action so that its output can be referenced in the input to other actionshisto5GRID_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. More detailsARG=the input for this action is the scalar output from one or more other actionsNPxxYBANDWIDTH=0.006the bandwidths for kernel density estimationLOGWEIGHTS=list of actions that calculates log weights that should be used to weight configurations when calculating averagesbiasLABEL=a label for the action so that its output can be referenced in the input to other actionshisto6GRID_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. More detailsARG=the input for this action is the scalar output from one or more other actionsPIF_aBANDWIDTH=0.01the bandwidths for kernel density estimationLOGWEIGHTS=list of actions that calculates log weights that should be used to weight configurations when calculating averagesbiasLABEL=a label for the action so that its output can be referenced in the input to other actionshisto7GRID_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. More detailsARG=the input for this action is the scalar output from one or more other actionsyyBANDWIDTH=0.035the bandwidths for kernel density estimationbiasLABEL=a label for the action so that its output can be referenced in the input to other actionshisto9GRID_MIN=0.30the lower bounds for the gridGRID_MAX=2.10the upper bounds for the gridGRID_BIN=150 ...the number of bins for the gridff5:CONVERT_TO_FESConvert a histogram, H(x), to a free energy surface using F(x) = -k_B T ln H(x). More detailsGRID=the action that creates the input grid you would like to usehisto5TEMP=310the temperature at which you are operatingDUMPGRIDOutput the function on the grid to a file with the PLUMED grid format. More detailsGRID=the action that creates the grid you would like to outputff5FILE=mw_fes_5ht1a_rec_tm3-tm6_1.datthe file on which to write the gridff6:CONVERT_TO_FESConvert a histogram, H(x), to a free energy surface using F(x) = -k_B T ln H(x). More detailsGRID=the action that creates the input grid you would like to usehisto6TEMP=310the temperature at which you are operatingDUMPGRIDOutput the function on the grid to a file with the PLUMED grid format. More detailsGRID=the action that creates the grid you would like to outputff6FILE=mw_fes_5ht1a_rec_NPxxY.datthe file on which to write the gridff7:CONVERT_TO_FESConvert a histogram, H(x), to a free energy surface using F(x) = -k_B T ln H(x). More detailsGRID=the action that creates the input grid you would like to usehisto7TEMP=310the temperature at which you are operatingDUMPGRIDOutput the function on the grid to a file with the PLUMED grid format. More detailsGRID=the action that creates the grid you would like to outputff7FILE=mw_fes_5ht1a_rec_PIF_a.datthe file on which to write the gridff9:Convert a histogram, H(x), to a free energy surface using F(x) = -k_B T ln H(x). More detailsGRID=the action that creates the input grid you would like to usehisto9TEMP=310the temperature at which you are operatingDUMPGRIDOutput the function on the grid to a file with the PLUMED grid format. More detailsGRID=the action that creates the grid you would like to outputff9FILE=mw_fes_5ht1a_rec_yy.datthe file on which to write the grid