RedMD/RedMDStream

Overview

RedMDStream is a piece of software used to develop models of biomolecular systems to be used with RedMD, a molecular simulation engine.

Availability

Cluster	Module/Version
BOSE	redmd/2.3 redmdstream/1.0
BGSC	Not Available

Note: You can simply use module load redmd and module load redmdstream to activate the most recently installed version of this software.

Sample Slurm Script

submit.sh

#!/bin/bash
# -- SLURM SETTINGS -- #
# [..] other settings here [..]

# The following settings are for the overall request to Slurm
#SBATCH --ntasks-per-node=32     # How many CPU cores do you want to request
#SBATCH --nodes=1                # How many nodes do you want to request

# -- SCRIPT COMMANDS -- #

# Load the needed modules
module load redmd/2.3  # Load redmd simulation engine
module load redmdstream/1.0 #Load redmdstream

Real Example

Has your research group used redmd/redmdstream in a project? Contact the HPC Team and we'd be glad to feature your work.

Citation

Please include the following citation in your papers to support continued development of redmd/redmdstream.

Adam Gorecki, Marcin Szypowski, Maciej Dlugosz, Joanna Trylska, RedMD – reduced molecular dynamics package RedMD – reduced molecular dynamics package, J. Comput. Chem., 30:2364-2373, 2009

Resources

• Official Website
• Documentation