Information about software packages installed on the ICHEC systems.
PLUMED is an open source library for free energy calculations in molecular systems which works together with some of the most popular molecular dynamics engines. Free energy calculations can be performed as a function of many order parameters with a particular focus on biological problems, using state of the art methods such as metadynamics, umbrella sampling and Jarzynski-equation based steered MD.
The PLUMED package is available for use by all ICHEC users.
To use PLUMED on Fionn, load the relevant environment module:
PLUMED has been added to the following list of codes on Fionn: NAMD 2.9, LAMMPS 1Feb14, GROMACS 4.6.5.
NAMD 2.9 Interface::
module load molmodel namd/intel/2.9
Executables are namd2_mpi_plumed for MPI and namd2_cuda_plumed for the CUDA version.
For details about submitting NAMD jobs on Fionn: NAMD Software.
LAMMPS 1Feb14 Interface:
module load molmodel lammps/intel/1Feb14
Executables are lmp_plumed for MPI and lmp_gpu_plumed for the CUDA version.
For details about submitting LAMMPS jobs on Fionn: LAMMPS Software.
GROMACS 4.6.5 Interface:
module load molmodel gromacs/intel/4.6.5
For details about submitting GROMACS jobs on Fionn: GROMACS Software.
More information can be obtained at the PLUMED Documentation available from the PLUMED webpage.