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Running the first membrane simulation
These are based off running on DT2. If running on MARCC see sample inputs from Dr. Klauda or others.
Once you've built the bilayer in CHARMM-GUI per Dr. Klauda's instructions you'll need to download that *tgz file a folder on DT2, so you can start to run the simulation. You MUST download the file and uncompress on DT2. Do NOT uncompress and then download…it will cause problems. You should uncompress the file with the tar -xvzf command and let Dr. Klauda (or an associated graduate student) know the path of this directory so I can have a quick check.
After approval of the setup, you will need to do is look at some files in the following directory on on DT2:
/homes/jbklauda/sim-inputs/namd/
The first-dyn.* files are good examples of setting up a set of membrane simulations that you should run in the namd subfolder that were made from CHARMM-GUI. This will run step6.1 to 6.6.
Changes in first-dyn.csh:
You will need to change the job-name to something relevant to you. On DT2, the example runs on a single 20-core node. You may adjust this and the associated lines from:
charmrun namd2 +p 19 +ppn 19 +setcpuaffinity
To changing the -N and -n in #SBATCH to the number of nodes that you are using. So for example if you are using 2 nodes the above part of the code will change:
mpirun -n 2 namd2 +auto-provision +setcpuaffinity
So the charmrun is removed and other and you only change '-n #' with # being the # of nodes.
Copy these first-dyn.* files directly to your namd subfolder. Then all you need to do is type:
./first-dyn.scr
And the job should be queued…you can check with
squeue -u username