PLUMED-NEST

Project ID: plumID:21.013
Source: ch4-base/symm-sample/plumed.inp
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

UNITS
This command sets the internal units for the code. More details
 
LENGTH
the units of lengths
=A 
TIME
the units of time
=fs 
ENERGY
the units of energy
=kcal/mol

COORDINATION
Calculate coordination numbers. More details
 
GROUPA
First list of atoms
=1 
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=2 
D_0
 The d_0 parameter of the switching function
=0.85 
R_0
The r_0 parameter of the switching function
=0.25 
NN
 The n parameter of the switching function 
=1 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=vib1
The COORDINATION action with label vib1 calculates a scalar quantity
COORDINATION
Calculate coordination numbers. More details
 
GROUPA
First list of atoms
=1 
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=3 
D_0
 The d_0 parameter of the switching function
=0.85 
R_0
The r_0 parameter of the switching function
=0.25 
NN
 The n parameter of the switching function 
=1 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=vib2

The COORDINATION action with label vib2 calculates a scalar quantity
COORDINATIONNUMBER
Calculate the coordination numbers of atoms so that you can then calculate functions of the distribution of More details
 
SPECIESA
this keyword is used for colvars such as the coordination number
=2-5 
SPECIESB
this keyword is used for colvars such as the coordination number
=1 
D_0
 The d_0 parameter of the switching function
=0.85 
R_0
The r_0 parameter of the switching function
=0.25 
NN
 The n parameter of the switching function 
=1 
MEAN
take the mean of these variables
 
MOMENTS
calculate the moments of the distribution of collective variables
=2 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=nm
The COORDINATIONNUMBER action with label nm calculates the following quantities:
 Quantity   
 Description  
nm.mean
the mean value
nm.moment
the central moments of the distribution of values
RESTRAINT
Adds harmonic and/or linear restraints on one or more variables. More details
 
ARG
the input for this action is the scalar output from one or more other actions
=nm.moment-2 
AT
the position of the restraint
=0.0 
KAPPA
 specifies that the restraint is harmonic and what the values of the force constants on each of the variables are
=200000000 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=restraint

The RESTRAINT action with label restraint calculates the following quantities:
 Quantity   
 Description  
restraint.bias
the instantaneous value of the bias potential
restraint.force2
the instantaneous value of the squared force due to this bias potential
HISTOGRAM
Accumulate the average probability density along a few CVs from a trajectory. More details
 ...
  
ARG
the input for this action is the scalar output from one or more other actions
=nm.mean
  
GRID_MIN
the lower bounds for the grid
=0.0
  
GRID_MAX
the upper bounds for the grid
=1.0
  
GRID_BIN
the number of bins for the grid
=2000
  
BANDWIDTH
the bandwidths for kernel density estimation
=0.005
  
LABEL
a label for the action so that its output can be referenced in the input to other actions
=targetdist
... HISTOGRAM

The HISTOGRAM action with label targetdist calculates a scalar quantity
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
=targetdist 
FILE
 the file on which to write the grid
=histo 
STRIDE
 the frequency with which the grid should be output to the file
=500000

FLUSH
This command instructs plumed to flush all the open files with a user specified frequency. More details
 
STRIDE
the frequency with which all the open files should be flushed
=100000
PRINT
Print quantities to a file. More details
 
ARG
the input for this action is the scalar output from one or more other actions
=vib1,vib2,nm.moment-2,nm.mean 
STRIDE
 the frequency with which the quantities of interest should be output
=50000 
FILE
the name of the file on which to output these quantities
=colvar