membrane_simulation
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membrane_simulation [2016/11/16 15:25] – admin | membrane_simulation [2023/08/17 16:08] (current) – admin | ||
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[[bilayer_simulations]] | [[bilayer_simulations]] | ||
- | Here are instructions for running | + | ==== Running |
+ | |||
- | Once you've built the bilayer in CHARMM-GUI per Dr. Klauda' | + | These are based off running on Zaratan. If running |
- | After approval of the setup, | + | Once you've built the bilayer in CHARMM-GUI per Dr. Klauda' |
- | ///homes/jbklauda/ | + | After approval of the setup, you will need to do is copy all the files in the following directory on Zaratan to your namd subfolder of the system you built: |
+ | |||
+ | //~jbklauda/ | ||
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. | 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. | ||
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Changes in // | Changes in // | ||
- | You will need to change the job-name to something relevant to you. The example on DT1 will run the simulations on 1 node (-N 1) with 8 cores (--ntasks=8). On DT2, the example runs on a single 20-core | + | You will need to change the job-name to something relevant to you. On Zaratan, there are 128-core nodes. For small bilayers (<30,000 atoms) |
+ | |||
+ | <code commend> charmrun namd2 +p 48 +ppn 48 +setcpuaffinity </ | ||
+ | |||
+ | If you wanted to use all the cores on the node then you would replace 48 with 128 in the .csh file (# | ||
- | <code commend> mpirun -np 8 </ | + | <code commend> mpirun --mca opal_warn_on_missing_libcuda -n 16 namd2 ++ppn 16 </ |
- | to run on more cores but for now let's start with this value. | + | So the charmrun is removed and other and you only change |
Copy these first-dyn.* files directly to your namd subfolder. | Copy these first-dyn.* files directly to your namd subfolder. |
membrane_simulation.1479327903.txt.gz · Last modified: 2016/11/16 15:25 (external edit)