Project ID: plumID:20.026
Source: plumed_WTMD.dat
Originally used with PLUMED version: 2.5
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 onv2.8
tested onmaster
rmsd_a: 
MULTI_RMSD
Calculate the RMSD distance moved by a number of separated domains from their positions in a reference structure. More details
REFERENCE
a file in pdb format containing the reference structure and the atoms involved in the CV
=OBP_lis_final.pdb
TYPE
the manner in which RMSD alignment is performed
=MULTI-OPTIMAL rmsd_b:
MULTI_RMSD
Calculate the RMSD distance moved by a number of separated domains from their positions in a reference structure. More details
REFERENCE
a file in pdb format containing the reference structure and the atoms involved in the CV
=OBP_lsd_final.pdb
TYPE
the manner in which RMSD alignment is performed
=MULTI-OPTIMAL
METAD
Used to performed metadynamics on one or more collective variables. More details
...
LABEL
a label for the action so that its output can be referenced in the input to other actions
=metad
ARG
the input for this action is the scalar output from one or more other actions
=rmsd_a,rmsd_b
SIGMA
the widths of the Gaussian hills
=0.01,0.01
HEIGHT
the heights of the Gaussian hills
=1.0
TEMP
the system temperature - this is only needed if you are doing well-tempered metadynamics
=310.15
PACE
the frequency for hill addition
=100
GRID_MIN
the lower bounds for the grid
=0,0
GRID_MAX
the upper bounds for the grid
=1.1,1.1
GRID_BIN
the number of bins for the grid
=400,400
BIASFACTOR
use well tempered metadynamics and use this bias factor
=5
CALC_RCT
calculate the c(t) reweighting factor and use that to obtain the normalized bias [rbias=bias-rct]
RCT_USTRIDE
the update stride for calculating the $c(t) $ reweighting factor
=10
FILE
a file in which the list of added hills is stored
=hills ... METAD
PRINT
Print quantities to a file. More details
STRIDE
the frequency with which the quantities of interest should be output
=100
ARG
the input for this action is the scalar output from one or more other actions
FILE
the name of the file on which to output these quantities
=colvar 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
=310.15
HISTOGRAM
Accumulate the average probability density along a few CVs from a trajectory. More details
...
LABEL
a label for the action so that its output can be referenced in the input to other actions
=hist
ARG
the input for this action is the scalar output from one or more other actions
=rmsd_a,rmsd_b
GRID_MIN
the lower bounds for the grid
=0,0
GRID_MAX
the upper bounds for the grid
=1.1,1.1
GRID_BIN
the number of bins for the grid
=400,400
BANDWIDTH
the bandwidths for kernel density estimation
=0.05,0.05
LOGWEIGHTS
list of actions that calculates log weights that should be used to weight configurations when calculating averages
=bias ... HISTOGRAM fes:
CONVERT_TO_FES
Convert a histogram, H(x), to a free energy surface using F(x) = -k_B T ln H(x). More details
GRID
the action that creates the input grid you would like to use
=hist
TEMP
the temperature at which you are operating
=310.15
DUMPGRID
Output the function on the grid to a file with the PLUMED grid format. More details
GRID
the action that creates the grid you would like to output
=fes
FILE
the file on which to write the grid
=fes
STRIDE
the frequency with which the grid should be output to the file
=1000000