PLUMED¶

PLUMED is a library that provides a wide range of methods for molecular dynamics (MD) simulations, such as enhanced-sampling algorithms and free-energy methods.

PLUMED is available as a module on Apocrita.

Usage¶

integration with other MD applications

PLUMED works together with some of the most popular MD engines, including but not limited to: CP2K, DL_POLY, GROMACS, LAMMPS and Quantum Espresso. These applications may already be installed on Apocrita, please see their respective documentation pages for more information.

To run the default installed version of PLUMED, simply load the plumed module:

$ module load plumed
$ plumed --help
Usage: plumed [options] [command] [command options]
  plumed [command] -h|--help: to print help for a specific command
Options:
  [help|-h|--help]          : to print this help
  [--is-installed]          : fails if plumed is not installed
  [--has-mpi]               : fails if plumed is running without MPI
  [--has-dlopen]            : fails if plumed is compiled without dlopen
  [--load LIB]              : loads a shared object (typically a plugin library)
  [--standalone-executable] : tells plumed not to look for commands implemented
                              as scripts

For full usage documentation, run plumed --help.

Example job¶

Serial job¶

Here is an example job running on 1 core and 1GB of memory.

#!/bin/bash
#$ -cwd
#$ -j y
#$ -pe smp 1
#$ -l h_rt=1:0:0
#$ -l h_vmem=1G

module load plumed

# analyse the trajectory "traj-whole.xtc", taken from a tutorial on
# the PLUMED website
plumed driver --plumed plumed.dat \
              --mf_xtc traj-whole.xtc

PLUMED¶

Usage¶

Example job¶

Serial job¶

References¶