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
tested onv2.10
tested onmaster
## Rebuild molecules that can become split by PBC
#
#MOLINFO  STRUCTURE=5ht1a_rec_ref.pdb
#WHOLEMOLECULES STRIDE=1 ENTITY0=1-4932

rbias:
READ
Read quantities from a colvar file. More details
FILE
the name of the file from which to read these quantities
=COLVAR
VALUES
the values to read from the file
=meta.rbias
IGNORE_TIME
ignore the time in the colvar file
tm3-tm6_1:
READ
Read quantities from a colvar file. More details
FILE
the name of the file from which to read these quantities
=COLVAR
VALUES
the values to read from the file
=tm3-tm6_1
IGNORE_TIME
ignore the time in the colvar file
NPxxY:
READ
Read quantities from a colvar file. More details
FILE
the name of the file from which to read these quantities
=COLVAR
VALUES
the values to read from the file
=NPxxY
IGNORE_TIME
ignore the time in the colvar file
yy:
READ
Read quantities from a colvar file. More details
FILE
the name of the file from which to read these quantities
=COLVAR
VALUES
the values to read from the file
=yy
IGNORE_TIME
ignore the time in the colvar file
PIF_a:
READ
Read quantities from a colvar file. More details
FILE
the name of the file from which to read these quantities
=COLVAR
VALUES
the values to read from the file
=PIF_a
IGNORE_TIME
ignore the time in the colvar file

bias:
REWEIGHT_METAD
Calculate the weights configurations should contribute to the histogram in a simulation in which a metadynamics bias acts upon the system. More details
TEMP
the system temperature
=310
HISTOGRAM
Accumulate the average probability density along a few CVs from a trajectory. More details
...
ARG
the quantities that are being used to construct the histogram
=tm3-tm6_1,yy
BANDWIDTH
the bandwidths for kernel density esimtation
=0.006,0.035
LOGWEIGHTS
the logarithm of the quantity to use as the weights when calculating averages
=bias
LABEL
a 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_BIN
the number of bins for the grid
=150,150 ...
HISTOGRAM
Accumulate the average probability density along a few CVs from a trajectory. More details
...
ARG
the quantities that are being used to construct the histogram
=tm3-tm6_1,NPxxY
BANDWIDTH
the bandwidths for kernel density esimtation
=0.006,0.006
LOGWEIGHTS
the logarithm of the quantity to use as the weights when calculating averages
=bias
LABEL
a 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_BIN
the number of bins for the grid
=150,150 ...
HISTOGRAM
Accumulate the average probability density along a few CVs from a trajectory. More details
...
ARG
the quantities that are being used to construct the histogram
=tm3-tm6_1,PIF_a
BANDWIDTH
the bandwidths for kernel density esimtation
=0.006,0.01
LOGWEIGHTS
the logarithm of the quantity to use as the weights when calculating averages
=bias
LABEL
a 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_BIN
the number of bins for the grid
=150,150 ...
ff1:
CONVERT_TO_FES
Convert a histogram to a free energy surface. More details
GRID
the histogram that you would like to convert into a free energy surface (old syntax)
=histo1
TEMP
the temperature at which you are operating
=310
DUMPGRID
Output the function on the grid to a file with the PLUMED grid format. More details
GRID
the 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_FES
Convert a histogram to a free energy surface. More details
GRID
the histogram that you would like to convert into a free energy surface (old syntax)
=histo2
TEMP
the temperature at which you are operating
=310
DUMPGRID
Output the function on the grid to a file with the PLUMED grid format. More details
GRID
the 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_FES
Convert a histogram to a free energy surface. More details
GRID
the histogram that you would like to convert into a free energy surface (old syntax)
=histo3
TEMP
the temperature at which you are operating
=310
DUMPGRID
Output the function on the grid to a file with the PLUMED grid format. More details
GRID
the 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