NAMD -- Scalable Molecular Dynamics

Motivation

The NAMD molecular parallel molecular dynamics package is supported from the University of Illinois NCSA as part of the NIH bioinformatics software effort. It scales to use some dozens of processors using gigabit ethernet. It uses VMD for simulation setup, but is also file-compatible with AMBER, CHARMM and X-PLOR.

Using NAMD
To load NAMD, type


source /usr/local/apps/NAMD/namd210.sh

If the file bnamd2 is in the same directory as the input file energies.conf, then executing the command


bsub < bnamd2


will execute NAMD. The file bnamd2 is as follows:


#!/bin/bash
#BSUB -o o.%J
#BSUB -e e.%J
#BSUB -W 15
#BSUB -R "span[ptile=4]"
#BSUB -n 4
source /usr/local/apps/NAMD/namd210.sh
mpirun namd2 ubq_wb_eq.conf > ubq_wb_eq.log


The flag "-W 15" requests at most 15 minutes. The flag "-n 4" requests 4 processors. In this case only one blade is used (due to the "-R span[ptile=4]" flag which specifies 4 cores on a blade be used.)
Links to Tutorial and Documentation

For some tutorials and example codes for using NAMD, see NAMD tutorial and NAMD home page.

A few sample runs can be found in /home/gwhowell/apps/samples/namd-tutorial-files.

cd /home/gwhowell/apps/samples
tar cvf pathyouwanttoputthetarfile/namd-tutorial-files.tar namd-tutorial-files
cd pathyouwanttoputhetarfile
tar xvf namd-tutorial-files.tar 
cd namd-tutorial-files

In the directory 2-3-energies there are some sample "btry" files which successfully run namd in some sample cases. The user need only change the paths for the -o and -e standard output and error.

Last modified: November 03 2025 23:36:08.