PLUMED-NEST

Project ID: plumID:21.013
Source: ch4-base/bend-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

ANGLES
Calculate functions of the distribution of angles . More details
 
GROUPA
A group of central atoms about which angles should be calculated
=1 
GROUPB
When used in conjunction with GROUPA this keyword instructs plumed to calculate all distinct angles involving one atom from GROUPA and two atoms from GROUPB
=2-5 
BETWEEN
calculate the number of values that are within a certain range
={GAUSSIAN LOWER=0.5pi UPPER=0.7pi} 
SWITCH
A switching function that ensures that only angles between atoms that are within a certain fixed cutoff are calculated
={RATIONAL D_0=1.50 R_0=0.25} 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=ang

The ANGLES action with label ang calculates the following quantities:
 Quantity   
 Description  
ang.between
the number/fraction of values within a certain range
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
=ang.between
  
GRID_MIN
the lower bounds for the grid
=1.0
  
GRID_MAX
the upper bounds for the grid
=4.5
  
GRID_BIN
the number of bins for the grid
=3500
  
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
=ang.between 
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