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 details FILEthe name of the file from which to read these quantities=COLVAR VALUESthe values to read from the file=meta.rbias IGNORE_TIME ignore the time in the colvar file tm3-tm6_1: READRead quantities from a colvar file. More details FILEthe name of the file from which to read these quantities=COLVAR VALUESthe values to read from the file=tm3-tm6_1 IGNORE_TIME ignore the time in the colvar file NPxxY: READRead quantities from a colvar file. More details FILEthe name of the file from which to read these quantities=COLVAR VALUESthe values to read from the file=NPxxY IGNORE_TIME ignore the time in the colvar file yy: READRead quantities from a colvar file. More details FILEthe name of the file from which to read these quantities=COLVAR VALUESthe values to read from the file=yy IGNORE_TIME ignore the time in the colvar file PIF_a: READRead quantities from a colvar file. More details FILEthe name of the file from which to read these quantities=COLVAR VALUESthe values to read from the file=PIF_a IGNORE_TIME ignore 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 details TEMPthe system temperature=310 HISTOGRAMAccumulate the average probability density along a few CVs from a trajectory. More details ... ARGthe quantities that are being used to construct the histogram=tm3-tm6_1,yy BANDWIDTHthe bandwidths for kernel density esimtation=0.006,0.035 LOGWEIGHTSthe logarithm of the quantity to use as the weights when calculating averages=bias LABELa label for the action so that its output can be referenced in the input to other actions=histo1 GRID_MIN the lower bounds for the grid=0.5,0.2 GRID_MAX the upper bounds for the grid=2.0,2.2 GRID_BINthe number of bins for the grid=150,150 ...
HISTOGRAMAccumulate the average probability density along a few CVs from a trajectory. More details ... ARGthe quantities that are being used to construct the histogram=tm3-tm6_1,NPxxY BANDWIDTHthe bandwidths for kernel density esimtation=0.006,0.006 LOGWEIGHTSthe logarithm of the quantity to use as the weights when calculating averages=bias LABELa label for the action so that its output can be referenced in the input to other actions=histo2 GRID_MIN the lower bounds for the grid=0.5,0.0 GRID_MAX the upper bounds for the grid=2.0,0.9 GRID_BINthe number of bins for the grid=150,150 ...
HISTOGRAMAccumulate the average probability density along a few CVs from a trajectory. More details ... ARGthe quantities that are being used to construct the histogram=tm3-tm6_1,PIF_a BANDWIDTHthe bandwidths for kernel density esimtation=0.006,0.01 LOGWEIGHTSthe logarithm of the quantity to use as the weights when calculating averages=bias LABELa label for the action so that its output can be referenced in the input to other actions=histo3 GRID_MIN the lower bounds for the grid=0.5,-0.05 GRID_MAX the upper bounds for the grid=2.0,0.7 GRID_BINthe number of bins for the grid=150,150 ...
ff1: CONVERT_TO_FESConvert a histogram to a free energy surface. More details GRIDthe histogram that you would like to convert into a free energy surface (old syntax)=histo1 TEMPthe temperature at which you are operating=310 DUMPGRIDOutput the function on the grid to a file with the PLUMED grid format. More details GRIDthe grid you would like to print (can also use ARG for specifying what is being printed)=ff1 FILE the file on which to write the grid=mw_fes_5ht1a_rec_tm3-tm6_yy.dat ff2: CONVERT_TO_FESConvert a histogram to a free energy surface. More details GRIDthe histogram that you would like to convert into a free energy surface (old syntax)=histo2 TEMPthe temperature at which you are operating=310 DUMPGRIDOutput the function on the grid to a file with the PLUMED grid format. More details GRIDthe grid you would like to print (can also use ARG for specifying what is being printed)=ff2 FILE the file on which to write the grid=mw_fes_5ht1a_rec_tm3-tm6_NPxxY.dat ff3: CONVERT_TO_FESConvert a histogram to a free energy surface. More details GRIDthe histogram that you would like to convert into a free energy surface (old syntax)=histo3 TEMPthe temperature at which you are operating=310 DUMPGRIDOutput the function on the grid to a file with the PLUMED grid format. More details GRIDthe grid you would like to print (can also use ARG for specifying what is being printed)=ff3 FILE the file on which to write the grid=mw_fes_5ht1a_rec_tm3-tm6_PIF.dat