PLUMED-NEST

Project ID: plumID:23.016
Source: plumed_reweight_2D_microsw_adr_bin.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

#MOLINFO  STRUCTURE=adr_bin_ref.pdb

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
The READ action with label rbias calculates the following quantities:
 Quantity   
 Description  
rbias..#!custom
the names of the output components for this action depend on the actions input file see the example inputs below for detailsNPxxY_i: 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_i IGNORE_TIME ignore the time in the colvar file
The READ action with label NPxxY_i calculates the following quantities:
 Quantity   
 Description  
NPxxY_i..#!custom
the names of the output components for this action depend on the actions input file see the example inputs below for detailstm3-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
The READ action with label tm3-tm6_1 calculates the following quantities:
 Quantity   
 Description  
tm3-tm6_1..#!custom
the names of the output components for this action depend on the actions input file see the example inputs below for detailsyy: 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
The READ action with label yy calculates the following quantities:
 Quantity   
 Description  
yy..#!custom
the names of the output components for this action depend on the actions input file see the example inputs below for detailsPIF_i: 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_i IGNORE_TIME ignore the time in the colvar file

The READ action with label PIF_i calculates the following quantities:
 Quantity   
 Description  
PIF_i..#!custom
the names of the output components for this action depend on the actions input file see the example inputs below for detailsbias: 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

The REWEIGHT_METAD action with label bias calculates the following quantities:
 Quantity   
 Description  
bias.value
the weight to use for this frame to negate the effect the metadynamics biasHISTOGRAMAccumulate 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=0.02,0.02
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=0.53,0.29
GRID_MAX the upper bounds for the grid=1.85,1.80
GRID_BINthe number of bins for the grid=150,150
...

The HISTOGRAM action with label histo1 calculates the following quantities:
 Quantity   
 Description  
histo1.value
the estimate of the histogram as a function of the argument that was obtainedHISTOGRAMAccumulate 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_i
BANDWIDTHthe bandwidths for kernel density esimtation=0.02,0.02
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=0.53,0.06
GRID_MAX the upper bounds for the grid=1.85,0.72
GRID_BINthe number of bins for the grid=150,150
...

The HISTOGRAM action with label histo2 calculates the following quantities:
 Quantity   
 Description  
histo2.value
the estimate of the histogram as a function of the argument that was obtainedHISTOGRAMAccumulate 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_i
BANDWIDTHthe bandwidths for kernel density esimtation=0.02,0.02
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=0.53,0.0
GRID_MAX the upper bounds for the grid=1.85,0.74
GRID_BINthe number of bins for the grid=150,150
...

The HISTOGRAM action with label histo3 calculates the following quantities:
 Quantity   
 Description  
histo3.value
the estimate of the histogram as a function of the argument that was obtainedff1: 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
The CONVERT_TO_FES action with label ff1 calculates the following quantities:
 Quantity   
 Description  
ff1.value
the free energy surfaceDUMPGRIDOutput 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_adr_bin_tm3-tm6_yy.dat

The DUMPGRID action with label  calculates somethingff2: 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
The CONVERT_TO_FES action with label ff2 calculates the following quantities:
 Quantity   
 Description  
ff2.value
the free energy surfaceDUMPGRIDOutput 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_adr_bin_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
The CONVERT_TO_FES action with label ff3 calculates the following quantities:
 Quantity   
 Description  
ff3.value
the free energy surfaceDUMPGRIDOutput 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_adr_bin_tm3-tm6_PIF.dat