PLUMED-NEST

Project ID: plumID:23.016
Source: plumed_reweight_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 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 detailstm3-tm6_2: 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_2 IGNORE_TIME ignore the time in the colvar file 
The READ action with label tm3-tm6_2 calculates the following quantities:
 Quantity   
 Description  
tm3-tm6_2..#!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 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 detailstm5: 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=tm5 IGNORE_TIME ignore the time in the colvar file 

The READ action with label tm5 calculates the following quantities:
 Quantity   
 Description  
tm5..#!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
BANDWIDTHthe bandwidths for kernel density esimtation=0.015
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=histo5
GRID_MIN the lower bounds for the grid=0.58
GRID_MAX the upper bounds for the grid=1.78
GRID_BINthe number of bins for the grid=150
...

The HISTOGRAM action with label histo5 calculates the following quantities:
 Quantity   
 Description  
histo5.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=NPxxY_i
BANDWIDTHthe bandwidths for kernel density esimtation=0.007
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=histo6
GRID_MIN the lower bounds for the grid=0.146
GRID_MAX the upper bounds for the grid=0.644
GRID_BINthe number of bins for the grid=150
...

The HISTOGRAM action with label histo6 calculates the following quantities:
 Quantity   
 Description  
histo6.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=PIF_i
BANDWIDTHthe bandwidths for kernel density esimtation=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=histo7
GRID_MIN the lower bounds for the grid=0.08
GRID_MAX the upper bounds for the grid=0.674
GRID_BINthe number of bins for the grid=150
...

The HISTOGRAM action with label histo7 calculates the following quantities:
 Quantity   
 Description  
histo7.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=yy
BANDWIDTHthe bandwidths for kernel density esimtation=0.03
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=histo9
GRID_MIN the lower bounds for the grid=0.33
GRID_MAX the upper bounds for the grid=1.78
GRID_BINthe number of bins for the grid=150
...

The HISTOGRAM action with label histo9 calculates the following quantities:
 Quantity   
 Description  
histo9.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=tm5
BANDWIDTHthe bandwidths for kernel density esimtation=0.03
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=histo10
GRID_MIN the lower bounds for the grid=0.73
GRID_MAX the upper bounds for the grid=1.66
GRID_BINthe number of bins for the grid=150
...

The HISTOGRAM action with label histo10 calculates the following quantities:
 Quantity   
 Description  
histo10.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_2
BANDWIDTHthe bandwidths for kernel density esimtation=0.015
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=histo13
GRID_MIN the lower bounds for the grid=0.88
GRID_MAX the upper bounds for the grid=2.19
GRID_BINthe number of bins for the grid=150

...


The HISTOGRAM action with label histo13 calculates the following quantities:
 Quantity   
 Description  
histo13.value
the estimate of the histogram as a function of the argument that was obtainedff5: 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)=histo5 TEMPthe temperature at which you are operating=310
The CONVERT_TO_FES action with label ff5 calculates the following quantities:
 Quantity   
 Description  
ff5.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)=ff5 FILE the file on which to write the grid=mw_fes_adr_bin_tm3-tm6_1.dat

The DUMPGRID action with label  calculates somethingff6: 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)=histo6 TEMPthe temperature at which you are operating=310
The CONVERT_TO_FES action with label ff6 calculates the following quantities:
 Quantity   
 Description  
ff6.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)=ff6 FILE the file on which to write the grid=mw_fes_adr_bin_NPxxY.dat

ff7: 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)=histo7 TEMPthe temperature at which you are operating=310
The CONVERT_TO_FES action with label ff7 calculates the following quantities:
 Quantity   
 Description  
ff7.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)=ff7 FILE the file on which to write the grid=mw_fes_adr_bin_PIF_i.dat

ff9: 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)=histo9 TEMPthe temperature at which you are operating=310
The CONVERT_TO_FES action with label ff9 calculates the following quantities:
 Quantity   
 Description  
ff9.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)=ff9 FILE the file on which to write the grid=mw_fes_adr_bin_yy.dat

ff10: 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)=histo10 TEMPthe temperature at which you are operating=310
The CONVERT_TO_FES action with label ff10 calculates the following quantities:
 Quantity   
 Description  
ff10.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)=ff10 FILE the file on which to write the grid=mw_fes_adr_bin_tm5.dat

ff13: 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)=histo13 TEMPthe temperature at which you are operating=310
The CONVERT_TO_FES action with label ff13 calculates the following quantities:
 Quantity   
 Description  
ff13.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)=ff13 FILE the file on which to write the grid=mw_fes_adr_bin_tm3-tm6_2.dat