Difference between revisions of "NAMD"
From Montana Tech High Performance Computing
(Created page with "NAMD - Scaleable Molecular Dynamics[http://www.ks.uiuc.edu/Research/namd/] is available on the HPC system. To access NAMD, either load the NAMD module: module load namd/2.1...") |
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NAMD - Scaleable Molecular Dynamics[http://www.ks.uiuc.edu/Research/namd/] is available on the HPC system. | NAMD - Scaleable Molecular Dynamics[http://www.ks.uiuc.edu/Research/namd/] is available on the HPC system. | ||
| − | To access NAMD, either load the NAMD module: module load namd/ | + | To access NAMD, either load the NAMD module: <code>module load namd</code> |
Or set your path to access it in /opt/NAMD by adding the following to your .bashrc or .bash_profile: | Or set your path to access it in /opt/NAMD by adding the following to your .bashrc or .bash_profile: | ||
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export PATH | export PATH | ||
===Example Job Script=== | ===Example Job Script=== | ||
| − | : <code style=display:block>#!/bin/sh<br>#PBS -l nodes=1:ppn=16<br>#PBS -N NAMD-test<br>#PBS -d /home/mtech/''username/working_dir''<br>#PBS -m e<br>#PBS -M ''username@institution''.edu<br>#PBS -l walltime=01:00:00<br><br>module load namd | + | : <code style=display:block>#!/bin/sh<br>#PBS -l nodes=1:ppn=16<br>#PBS -N NAMD-test<br>#PBS -d /home/mtech/''username/working_dir''<br>#PBS -m e<br>#PBS -M ''username@institution''.edu<br>#PBS -l walltime=01:00:00<br><br>module load namd<br>charmrun namd2 +p16 xxxxx.conf > yyyyy.txt</code> |
Note: | Note: | ||
Latest revision as of 10:45, 18 September 2017
NAMD - Scaleable Molecular Dynamics[1] is available on the HPC system.
To access NAMD, either load the NAMD module: module load namd
Or set your path to access it in /opt/NAMD by adding the following to your .bashrc or .bash_profile: PATH=$PATH:/opt/NAMD/ export PATH
Example Job Script
-
#!/bin/sh
#PBS -l nodes=1:ppn=16
#PBS -N NAMD-test
#PBS -d /home/mtech/username/working_dir
#PBS -m e
#PBS -M username@institution.edu
#PBS -l walltime=01:00:00
module load namd
charmrun namd2 +p16 xxxxx.conf > yyyyy.txt
Note:
- charmrun must be the first statement in order to load CHARM++ to the run
- namd2 is the executable for NAMD
- +p<#processes> => number of processes that will run on the node = same as the ppn value on top
- xxxxx.conf => configuration file
- yyyyy.txt => write output to file since NAMD writes to standard out