29-Feb-2008

Introduction

NAMD is a parallel, object-oriented molecular dynamics code that is designed for high-performance simulation of large biomolecular systems. The version of NAMD on Ada has been compiled to take advantage of Ada's fast interconnect called RapidArray. Please follow the instructions below to use this version of NAMD on Ada.

Running NAMD with PBS

The steps for running NAMD with PBS on Ada are described below:

1. Prepare the Data Directory

Create a directory to store your input and output data files. In this example, the input and output files and the PBS script will all be stored in the same directory. This is not required but is presented this way here to simplify the instructions. Start by creating a working directory called NAMD, for example:

cd /home/adauser                      # go to your home directory
mkdir NAMD                            # create a work directory named NAMD

Create an NAMD configuration file in this directory and call it simulation.conf . Then create the input files required by the simulation.conf file, such as the PSF file (structure), coordinates file (PDB), and so forth and place them in your NAMD directory or at the path specified in your simulation.conf file. For more information on the structure of the configuration file, please see the NAMD User's Guide.

2. Initialize your Environment to run NAMD

In order to run NAMD, you need to initialize your environment using the module command as follows:

module load namd/2.6_RapidArray

This command will set the appropriate environment variables that you need to run NAMD. The version of NAMD referenced by the module command is a version specifically compiled to use Ada's high performance interconnect (RapidArray).

3. Prepare and Run the PBS Job

Once the data files are in place, create a PBS batch job script called NAMD.pbs in the same directory with the following contents:

#PBS -N NAMD
#PBS -q compute
#PBS -l nodes=2:ppn=4,walltime=08:00:00
#PBS -m n
#PBS -V           ## This line is important 
                  ## to inherit the correct environment variables
#PBS -M username@rice.edu

echo "My job ran on: "
cat $PBS_NODEFILE
cd $PBS_O_WORKDIR

mpiexec $XD1LAUNCHER namd2 ./simulation.conf > ./out.txt

This script assumes that all of your files (such as simulation.conf and out.txt) are in the same directory (your current working directory). If they are not, then you must specify the full path to the files.

Now run the PBS job from this working directory as follows:

qsub ./NAMD.pbs       # this will submit the job to the job scheduler

More Information (NAMD User's Guide)

For information about how to use NAMD, please see the NAMD User's Guide.