plumed

Invoke the PLUMED plugin during a MD run.

Syntax

This keyword has the following format:

plumed <plumed_file> <interval> <if_restart>

The plumed_file parameter is the name of the PLUMED input file. The interval parameter is the interval (number of steps) of calling the PLUMED subroutines. The if_restart parameter determines if the PLUMED plugin should restart its calculations, which includes appending to its output files, reading the previous biases, etc.

Requirements and specifications

  • This keyword requires an external package to operate. Instructions for how to set up the PLUMED package can be found here.

  • Increasing the interval parameter will speed up your simulation if you only want PLUMED to calculate collective variables (CVs). But you have to set it to 1 if your simulation was biased by PLUMED.

Examples

Example 1

To calculate the distance between atoms, one can add:

plumed plumed.dat 1000 0

before the run command. The plumed.dat file, for example, may look like:

UNITS LENGTH=A TIME=fs ENERGY=eV
FLUSH STRIDE=1
DISTANCE ATOMS=1,2 LABEL=d1
PRINT FILE=colvar ARG=d1

The output file created by PLUMED (the colvar file) will be updated every 1000 steps.

Example 2

To restrain the distance between atoms, one can add:

plumed plumed.dat 1 0

before the run command. The plumed.dat file, for example, may look like:

UNITS LENGTH=A TIME=fs ENERGY=eV
FLUSH STRIDE=1
DISTANCE ATOMS=1,2 LABEL=d1
RESTRAINT ARG=d1 AT=0.0 KAPPA=2.0 LABEL=restraint
PRINT FILE=colvar ARG=d1,restraint.bias

Caveats

  • This keyword is not propagating. That means, its effect will not be passed from one run to the next.