Run NAMD on the Cluster¶
- NAnoscale Molecular Dynamics is computer software for molecular dynamics simulation written using the Charm++ parallel programming model.
- This guide will cover how to run NAMD on the Cluster.
- For more information about NAMD, please visit the NAMD Tutorial Page.
- NAMD uses a Protein Data Bank (pdb) file, a Protein Structure File (psf), a force field parameter file, and a configuration file to set up a molecular dynamics simulation.
Walkthrough: Run NAMD on the Cluster¶
- The example covered in this walkthrough will have the user examine the ApoA1 tutorial.
apoa1folder can be found here
SBATCHscript can be found here
Part 1: The SBATCH Script¶
#!/bin/bash #SBATCH -JnamdTest #SBATCH -A [Account] #SBATCH -N1 --ntasks-per-node=8 #SBATCH --mem-per-cpu=2G #SBATCH -t15 #SBATCH -qinferno #SBATCH -onamdOutput.out cd $SLURM_SUBMIT_DIR module load namd namd2 apoa1/apoa1.namd
#SBATCHdirectives are standard, requesting just 3 minutes of walltime and 1 node with 8 cores. More on
#SBATCHdirectives can be found in the Using Slurm on Phoenix Guide
$SLURM_SUBMIT_DIRis a variable that represents the directory you submit the SBATCH script from. Make sure the files you want to use are in the same directory you put the SBATCH script.
- Output Files will also show up in this dir as well
module load namd/2.14_ibverbsloads the 2.14 version of NAMD. To see what versions of a software are available, run
module avail [Software], and load the one you want. The other modules are dependencies that must be loaded before NAMD is loaded.
namd2 apoa1/apoa1.namdwill have Namd carry out the operation.
Part 2: Submit Job and Check Status¶
- Make sure you're in the dir that contains the
SBATCHScript as well as the
- Submit as normal, with
sbatch < script name>. In this case
- Check job status with
squeue --job <jobID>, replacing with the jobid returned after running sbatch
- You can delete the job with
scancel <jobID>, replacing with the jobid returned after running sbatch
Part 3: Collecting Results¶
- In the directory where you submitted the
SBATCHscript, you should see a
Report-<jobID>.outfile which contains the results of the job.
Report-<jobID>.outshould look like this
- After the result files are produced, you can move the files off the cluster, refer to the file transfer guide for help.
- Congratulations! You successfully ran NAMD on the cluster.