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

The UNITS action with label  calculates something
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 the following quantities:
 Quantity   
 Description  
vib1.value
the value of the coordination
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 the following quantities:
 Quantity   
 Description  
vib2.value
the value of the coordination
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
 calculate the mean of all the quantities
 
MOMENTS
the list of moments that you would like to calculate
=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 something
RESTRAINT
Adds harmonic and/or linear restraints on one or more variables. More details
 
ARG
the arguments on which the bias is acting
=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 something
HISTOGRAM
Accumulate the average probability density along a few CVs from a trajectory. More details
 ...
  
ARG
the quantity that is being averaged
=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 esimtation
=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 something
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)
=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