NAMD

This article is a draft

This is not a complete article: This is a draft, a work in progress that is intended to be published into an article, which may or may not be ready for inclusion in the main wiki. It should not necessarily be considered factual or authoritative.

General

NAMD is a parallel, object-oriented molecular dynamics code designed for high-performance simulation of large biomolecular systems. Simulation preparation and analysis is integrated into the visualization package VMD.

• Project web site: http://www.ks.uiuc.edu/Research/namd/
• Manual: http://www.ks.uiuc.edu/Research/namd/current/ug/
• Downloads: http://www.ks.uiuc.edu/Development/Download/download.cgi?PackageName=NAMD
• Tutorials: http://www.ks.uiuc.edu/Training/Tutorials/

A registration required to download software.

Release notes:

• Version 2.11: http://www.ks.uiuc.edu/Research/namd/2.11/notes.html

NAMD Wiki, How to compile: https://proteusmaster.urcf.drexel.edu/urcfwiki/index.php/Compiling_NAMD

Quickstart Guide

This section summarizes configuration details.

Environment Modules

The following modules providing NAMD are available on graham and cedar.

Compiled without CUDA support:

• namd-multicore/2.12
• namd-verbs/2.12

Compiled with CUDA support:

• namd-multicore/2.12
• namd-verbs-smp/2.12

To access these modules which require CUDA, first execute:

module load cuda/8.0.44

Note: using verbs library is more efficient than using OpenMPI, hence only verbs versions are provided.

Submission Scripts

These examples of submission scripts will still have to be tested once the national system are available for testing.

Please refer to the page "Running jobs" for help on using the SLURM workload manager.

Serial Job

Here's a simple job script for serial simulation:

File : serial_namd_job.sh

#!/bin/bash
#
#SBATCH --ntasks 1            # number of tasks
#SBATCH --mem 1024            # memory pool per process
#SBATCH -o slurm.%N.%j.out    # STDOUT
#SBATCH -t 0:20:00            # time (D-HH:MM)
#SBATCH --gres=gpu:1

module load namd-multicore/2.12
namd2 +p1 +idlepoll apoa1.namd

Verbs Job

Instructions will be provided once this configuration can be tested on the new clusters.

GPU Job

This example uses 8 CPU cores and 1 GPU on a single node.

File : multicore_gpu_namd_job.sh

#!/bin/bash
#
#SBATCH --ntasks 8            # number of tasks
#SBATCH --mem 1024            # memory pool per process
#SBATCH -o slurm.%N.%j.out    # STDOUT
#SBATCH -t 0:05:00            # time (D-HH:MM)
#SBATCH --gres=gpu:1

module load cuda/8.0.44
module load namd-multicore/2.12
namd2 +p8 +idlepoll apoa1.namd