PLUMED-NEST

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

## 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 
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 detailsNPxxY: 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
The READ action with label NPxxY calculates the following quantities:
 Quantity   
 Description  
NPxxY..#!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_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

The READ action with label PIF_a calculates the following quantities:
 Quantity   
 Description  
PIF_a..#!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=0.006,0.035
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
...

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
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
...

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_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
...

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 GRIDYou should use ARG instead of this keyword which was used in older versions of PLUMED and is provided for back compatibility only=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 GRIDYou should use ARG instead of this keyword which was used in older versions of PLUMED and is provided for back compatibility only=ff1 FILE the file on which to write the grid=mw_fes_5ht1a_rec_tm3-tm6_yy.dat

The DUMPGRID action with label  calculates somethingff2: CONVERT_TO_FESConvert a histogram to a free energy surface. More details GRIDYou should use ARG instead of this keyword which was used in older versions of PLUMED and is provided for back compatibility only=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 GRIDYou should use ARG instead of this keyword which was used in older versions of PLUMED and is provided for back compatibility only=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 GRIDYou should use ARG instead of this keyword which was used in older versions of PLUMED and is provided for back compatibility only=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 GRIDYou should use ARG instead of this keyword which was used in older versions of PLUMED and is provided for back compatibility only=ff3 FILE the file on which to write the grid=mw_fes_5ht1a_rec_tm3-tm6_PIF.dat