PLUMED-NEST

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

rmsd_a: 
MULTI_RMSD
Calculate RMSD distances for different domains and combine them. 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 RMSD distances for different domains and combine them. 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
The METAD action with label metad calculates the following quantities:
 Quantity   
 Description  
metad.bias
the instantaneous value of the bias potential
metad.rbias
the instantaneous value of the bias normalized using the c(t) reweighting factor [rbias=bias-rct]
metad.rct
the reweighting factor $c(t)$
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
The REWEIGHT_METAD action with label bias calculates a scalar quantity
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 quantity that is being averaged
=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 esimtation
=0.05,0.05 
LOGWEIGHTS
the logarithm of the quantity to use as the weights when calculating averages
=bias
... HISTOGRAM
fes: 
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)
=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 grid you would like to print (can also use ARG for specifying what is being printed)
=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