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NAMD - Molecular Dynamics of Large Biomolecules

Table of contents

Introduction and Licensing

NAMD is a molecular dynamics program designed for parallel computation. Full and efficient treatment of electrostatic and van der Waals interactions are provided via the Particle Mesh Ewald algorithm. NAMD interoperates with CHARMM and X-PLOR as it uses the same force field and includes a rich set of MD features (multiple time stepping, constraints, and dissipatitve dynamics). More information is available from the Theoretical Biophysics Group at the University of Illinois.

NAMD Molecular Dynamics Software Non-Exclusive, Non-Commercial Use License

Running NAMD at LRZ

The module package controls access to software. To use the default version of NAMD, please load the module environment appropriate first after login to the system via:

% module load namd

Please be advised that NAMD 2.7 (October 15, 2010) is currently available at LRZ.

Parallel and Sequential execution of NAMD

After the module is loaded you can run namd using

% namd -n 1 inputfilename   (sequential)
% namd -n N inputfilename   (parallel)

Running Parallel-NAMD on the Linux-Cluster

After login to the system, you should use a job script like this:

Parallel NAMD on the Linux-Cluster

 
#!/bin/bash
#$ -o $HOME/mydir/myjob.out -j y
#$ -N XXXX
#$ -l h_rt=10:00:00
#$ -M XXXX@mydomain    <your email address>
#$ -pe mpi_pe 8  <or: -pe numa* 8 for altix>
# can also use -pe mpi_ice up to 256 
#more details see examples
    . /etc/profile
 cd mydir            <link to your input>
 module load namd
 namd -n 8  my-job.inp

Then submit the job script using the qsub command, e.g. assuming the job script name is name-job.pbs,

% qsub  name-job.pbs

There are many other parameters to the batch system at LRZ. For more details see <a href="../../../compute/linux-cluster/batch_parallel/index.html>Running parallel jobs with SLURM

Running Parallel-NAMD on the superMIG

In order to start NAMD on superMIG with Np processes the IBM POE has to be used.

Load the module for namd:

bash> module load namd/2.8

Please note that versions before 2.8 are not available for superMUC.

Parallel Execution under POE (Parallel Operating Environment)

On the superMUC all parallel jobs (interactive and batch) are controlled by the POE. In order to start a parallel NAMD job using 80 cores on 2 compute nodes, the following environment variables have to be set for interactive execution or a loadleveler command file has to be generated for batch execution:

bash> export MP_NODES=2
bash> export MP_PROCS=80
bash> namd myscript.namd
starts an interactive NAMD job which has the script myscript.namd by using 2 compute nodes with a total of 80 cores. Note that each compute node on the superMIG has 40 cores which means that the number of procs has to be smaller than 40 times the number of nodes. Sometimes it might be necessary to chose the number of procs less than 40 times nodes due to memory considerations.

The loadleveler file could look like:

Parallel NAMD on SuperMIG

 
#!/bin/bash
#$ job_name = NAMD
#$ initialdir = $(work)/namd/
#$ output     = $(work)/namd/$(job_name).$(jobid).out
#$ error      = $(work)/namd/$(job_name).$(jobid).err
#$ job_type = parallel
#$ class = general
#$ wall_clock_limit = 24:00:00
#$ node = 4
#$ tasks_per_node = 40
#$ queue

. /etc/profile.d/modules.sh
 
module load namd/2.8
cd $(work)/namd/
namd2 my_md_start_file.namd

In this example, the number of cores and the number of nodes are infered from the job control directives in the upper part of the file, where nodes denotes the number of nodes and tasks_per_node denotes the number of tasks per node which should not exceed 40. Store these commands in a job command file with e.g. the file name myjob.sh


The job can then be submitted via the command:

bash> llsubmit myjob.sh

the job status can be monitored using the llq command. 

bash> llq

Documentation

  • After execution of module load namd, the environment variable documentation points to a directory containing the NAMD documentation as it comes with the source code:

    ls -C  $NAMD_DOC
    ls -C  $NAMD_SRC

  • Other format of the documentation and more information may be found on the NAMD-Homepage

Examples

After execution of module load namd, the environment variable EXAMPLES points to the NAMD examples:

ls -C $NAMD_EXAMPLES

Support

If you have any questions or problems with NAMD installed on the different LRZ platforms, please don't hesitate to contact LRZ HPC support staff .