PLUMED-NEST

Project ID: plumID:21.032
Source: plumed_water.dat
Originally used with PLUMED version: 2.6
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

WHOLEMOLECULES
This action is used to rebuild molecules that can become split by the periodic boundary conditions. More details
 
ENTITY0
the atoms that make up a molecule that you wish to align
=1-781 
STRIDE
 the frequency with which molecules are reassembled
=1

metad:       
READ
Read quantities from a colvar file. More details
 
FILE
the name of the file from which to read these quantities
=COLVAR_REWEIGHT_sol 
IGNORE_TIME
 ignore the time in the colvar file
 
VALUES
the values to read from the file
=metad.bias
The READ action with label metad calculates a scalar quantityweights1: 
REWEIGHT_BIAS
Calculate weights for ensemble averages that negate the effect the bias has on the region of phase space explored More details
 
TEMP
the system temperature
=300 
ARG
 the biases that must be taken into account when reweighting
=metad.bias

The REWEIGHT_BIAS action with label weights1 calculates a scalar quantityWAT: 
GROUP
Define a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details
 
ATOMS
the numerical indexes for the set of atoms in the group
=782-23020:3

WAT64:  
COORDINATION
Calculate coordination numbers. More details
 
SWITCH
This keyword is used if you want to employ an alternative to the continuous switching function defined above
={RATIONAL R_0=0.29 D_MAX=0.5 NN=12 MM=24} 
GROUPA
First list of atoms
=WAT 
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=776 




The COORDINATION action with label WAT64 calculates a scalar quantityCys: 
GROUP
Define a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details
 
ATOMS
the numerical indexes for the set of atoms in the group
=67,88,243,292,152,324,173,211,359,465,455,628,434,512,554,761,599,424,751,730


coord64: 
COORDINATION
Calculate coordination numbers. More details
  
GROUPA
First list of atoms
=Cys 
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=776 
SWITCH
This keyword is used if you want to employ an alternative to the continuous switching function defined above
={RATIONAL R_0=0.315 D_MAX=0.5 NN=12 MM=24}


The COORDINATION action with label coord64 calculates a scalar quantity
HISTOGRAM
Accumulate the average probability density along a few CVs from a trajectory. More details
 ...
   
ARG
the quantity that is being averaged
=coord64,WAT64
   
GRID_MIN
 the lower bounds for the grid
=0,0
   
GRID_MAX
 the upper bounds for the grid
=6,8
   
GRID_BIN
the number of bins for the grid
=300,300
   
BANDWIDTH
the bandwidths for kernel density esimtation
=0.05,0.05
   
LABEL
a label for the action so that its output can be referenced in the input to other actions
=h64
LOGWEIGHTS
the logarithm of the quantity to use as the weights when calculating averages
=weights1
... HISTOGRAM


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)
=h64 
FILE
 the file on which to write the grid
=histo_wall 
FMT
the format that should be used to output real numbers
=%24.16e

fes64: 
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)
=h64 
TEMP
the temperature at which you are operating
=300
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)
=fes64 
FILE
 the file on which to write the grid
=fes64opt.dat 
FMT
the format that should be used to output real numbers
=%8.4f

PRINT
Print quantities to a file. More details
 
STRIDE
 the frequency with which the quantities of interest should be output
=1 
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_coor_optim