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How to run NAMD (molecular dynamics simulation software) on cluster

Step 1: Please read "how to setup your working environment" and do the following:

a. Include the sentence of "module load namd/default" in the module-loading blocks in your .bashrc file

b. Type ". .bashrc" in your terminal, and then type "module list or type "which blastall" in your terminal again, you shall be able to see: 

[testy@n137 ~]$ . .bashrc
[testy@n137 ~]$ module list
Currently Loaded Modulefiles:
   1) namd/default
If you see the above output on terminal, it means your environment has been setup correctly.

c. Type ". .bashrc" in your terminal to enable the above configuration. To confirm your configuration is correct, type the following: 
[testy@n137 ~] which mpirun
/opt/hpmpi/bin/mpirun
[testy@n137 ~] which charmrun
/source/namd/charmrun
[testy@n137 ~] which namd2
/source/namd/namd2
Step 2: The following script namd_job.lsf is used to submit your Molecular Dynamics simulation on hpres cluster.

Notes: This script:

1) Setups the job parameter and assumes you will collect 8 CPUs and will use both CPU for each node

2) Creates "mynodefile" by interacting with LSF environment to generate the node list file for namd

3) Runs the program. (assuming runNAMD.conf is your namd input file)

#!/bin/bash

# enable your environment, which will use .bashrc configuration in your home directory
#BSUB -L /bin/bash

# the name of your job showing on the queue system
#BSUB -J namdtest

# the queue that you will use, the example here use the queue called "normal"
#BSUB -q long

# the system output and error message output, %J will show as your jobID
#BSUB -o %J.out
#BSUB -e %J.err

#the CPU number that you will collect (Attention: each node has 2 CPU)

#BSUB -n 8

#when job finish that you will get email notification. If you donot want email notification,
#simply delete the following lines, or replace your email with /dev/null
#BSUB -u youremail@partners.org
#BSUB -N


# setup your working environment. We need to interact with the LSF environment to get the
# hostfile for namd. A file called mynodefile will be created in your working directory


workdir=/shr/home/$USER/your_working_dir
cd $workdir

Ncpu=0
echo group main > mynodefile
for node in $LSB_HOSTS
do
  echo host $node >> mynodefile
  Ncpu=$(($Ncpu+1))
done


#Start the NAMD job, runNAMD.conf is my input file, mynamd.log is my
#namd log file, you can change these names
charmrun ++remote-shell ssh ++nodelist mynodefile +p$Ncpu  namd2 runNAMD.conf >& mynamd.log


Step 4: Submit the job 

[testy@n137 ~]$ bsub < namd_job.lsf


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