Introduction

Charmm is a computational chemistry program designed for modeling and simulation of molecular systems aimed specifically at modeling large multi-particle systems such as biomolecules.

Using Charmm on RCC Resources

Running Charmm Interactively

In order to run Charmm on RCC systems, both the GNU OpenMPI module and the Charmm module itself must be loaded before Charmm commands can be run. To run Charmm in interactive mode, for example, the following commands would be used:

module load gnu-openmpi
module load charmm

charmm

Running Charmm in Serial

In order to run Charmm on RCC systems in Serial, the following commands may be used:

module load charmm

charmm -i INFILE.inp >& OUTFILE.out

Running Charmm in Parallel

Charmm can also be run as a batch script using the Slurm scheduler.

module load gnu-openmpi
module load charmm

mpirun -np NPROCS charmm -i INFILE.inp >& OUTFILE.out

Our default installation of CHARMM is optimized for Intel processors and may not run effectively with large numbers of cores on our AMD nodes. To sidestep the issue, you can either run your job on the backfill partitions which are mostly Intel or you can add a hardware constraint to your batch script (#SBATCH -C). For example:

#!/bin/bash
#SBATCH -n 64
#SBATCH -p genacc_q
#SBATCH -t 14-00:00:00

#SBATCH -C "intel"

module load gnu-openmpi
module load charmm

srun charmm -i INFILE.inp >& OUTFILE.out

Detailed information on Charmm command-line usage can be found at the documentation site

Acknowledgement

RCC thanks Steven Austin from the Yang Laboratory for his generous contribution of a working test script and associated files which allowed us to run tests on the code on this page and the associated Submit Script Generator template.