Biowulf High Performance Computing at the NIH
CAMPARI on Biowulf

CAMPARI is a molecular simulation packages with a number of features, including the ability to perform virtual screening and docking applications as well as Monte Carlo and molecular dynamics simulations of biopolyers. Ir is primarily developed by the Papula lab at the Washington University of St. Louis with other contributions from the Caflisch lab at the University of Zurich. Version 4.0 was released in late 2020 and has been installed on Biowulf.

Quick links to docuentation:

SLURM Batch Jobs

Unlike other molecular dynamics packages, CAMPARI primarily runs as a serial (single CPU) process. The multi-threaded (OpenMP) code is considered experimental in nature and to be used only for development and testing/ Therefore, the version installed on Biowulf does not support this feature. However, certain jobs (such as replica exchange) can be run with task based parallelism using MPI. The correct MPI module for such jobs is loaded automatically when the campari module is loaded.

An example serial job

The following script shows how to subit a serial (single CPU) CAMPARI job that runs for at ost two days and executes a siulation defined in the run.key keyfile.

#!/bin/bash
#SBATCH --partition=norm
#SBATCH --time=2-0

module load campari/4.0

campari -k run.key >& run.out

Unfortunately, the HPC staff has not been able to get a Campari MPI job running correctly on our system. If you wish to run a Campari MPI job on Biowulf, please e-mail staff@hpc.nih.gov, and we will work with you to attempt to run your job. Please include the key file that you wish to execurte with this e-mail.

Parameter files

Campari supports numerous different molecular mechanics and coarsed grained force fields. The parameter files are in /usr/local/apps/campari/4.0/params.

Usage examples

Campari provides a set of tutorial inputs, which are located at /usr/local/apps/campari/4.0/exampless. Please note that these example inputs are not complete and that further effort on the part of the user is needed to make an actual working batch submission from these files. In particular, users must consult the online tutorial resources for information on how to correctly use the tutorial inputs.