Contents


Deprecated: please see new documentation site.



Introduction

"NAMD is a parallel, object-oriented molecular dynamics code designed for high-performance simulation of large biomolecular systems."

Version and availability

The parallel version of NAMD 2.6 & 2.7b2 is available on all LONI x86 clusters (Eric, Oliver, Louie, Painter, Poseidon and Queen Bee).

Usage

We currently have two versions of NAMD installed under /usr/local/packages/NAMD: v2.6 and v2.7b2, both built with MVAPICH.

To use v2.6, make sure you have these line of your .soft file (For TeraGrid users: these lines need to appear before the "@teragrid-xxx" macros):

 +tcl-8.3.4-intel-11.1
 +NAMD-2.6-intel-11.1-mvapich-1.1
 +mvapich-1.1-intel-11.1

To use v2.7b2, use these lines instead (again, they should appear before the "@teragrid-xxx" macros):

 +tcl-8.3.4-intel-11.1
 +NAMD-2.7b2-intel-11.1-mvapich-1.1
 +mvapich-1.1-intel-11.1

Don't forget to resoft

To run NAMD through PBS, you need a script like the one below (for the MVAPICH version):

 #!/bin/sh
 
 #PBS -A your_allocation
 #PBS -q checkpt
 #PBS -M your_email
 # Change ppn to 8 if running on Queen Bee
 #PBS -l nodes=4:ppn=4
 #PBS -l walltime=06:00:00
 #PBS -V
 #PBS -o NAMD_test.out
 #PBS -e NAMD_test.err
 #PBS -N namdtest
  
 export EXEC=namd2
 export EXEC_DIR=/usr/local/packages/NAMD/2.6/intel-11.1-mvapich-1.1
 export WORKDIR=$PBS_O_WORKDIR
 export NPROCS=`wc -l $PBS_NODEFILE | gawk '//{print $1}'`
 export CONV_RSH=ssh
 cd $WORKDIR
  
 mpirun -machinefile $PBS_NODEFILE -np $NPROCS $EXEC_DIR/$EXEC apoa1.namd

Then submit it to run (assuming that the script above is namd.pbs):

 qsub namd.pbs

References

NAMD Users Guide is available on line.


Users may direct questions to sys-help@loni.org.

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