NAMD

General Information

Home pageVersionModule dependencies
CompilerMPT
www.ks.uiuc.edu/Research/namd2.10intelcomp/15.0.1mpt/2.10
2.11intelcomp/16.0.1mpt/2.13
2.12intelcomp/17.0.0mpt/2.14

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

Usage on Vilje

Load one of the namd, and the corresponding intel compiler and mpt modules to use NAMD on Vilje, e.g:

$ module load intelcomp/17.0.0 mpt/2.14 namd/2.12

Sample NAMD Job Script

#!/bin/bash
###################################################
#
#  NAMD job
#
###################################################
#
#PBS -N test
#PBS -A nn1234k
#PBS -l select=2:ncpus=32:mpiprocs=16
#PBS -l walltime=24:00:00
#
 
module load intelcomp/17.0.0
module load mpt/2.14
module load namd/2.12
 
case=$PBS_JOBNAME
 
cd $PBS_O_WORKDIR
 
# Create (if necessary) the working directory
w=/work/$PBS_O_LOGNAME/namd/$case
if [ ! -d $w ]; then mkdir -p $w; fi
 
# Copy inputfiles and move to working directory
cp $case.* $w
cd $w

ulimit -s 300000

mpiexec_mpt namd2 $case.namd

Test case: Ubiquitin in a Water Sphere

This example examines the minimization and equilibration of ubiquitin in a water sphere placed in vacuum.

See sections 3-7 at the NAMD Tutorials web page for a detailed description of the input file.

1. Unpack the test case files

$ tar xf /sw/sdev/Modules/namd/2.12/share/ubq_ws.tar

2. Replace nn1234k with your project account number in the namd.pbs job script, and submit the job to the queuing system

$ qsub namd.pbs

3. When the job has finished, check the output file and compare with the output ubq_ws.out included in test case. See also a description of the Water Sphere output files. (The content of the ubq_ws_eq.log desbribed is saved in your standard output file from the job.)

Further Information

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