production_run
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production_run [2016/09/20 12:15] – admin | production_run [2022/09/28 17:23] (current) – admin | ||
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[[bilayer_simulations]] | [[bilayer_simulations]] | ||
- | Here are production | + | ==== Production |
- | Listed below are some instructions for the production run simulation. As we discussed, this will automatically run your simulation in chunks with each being a certain length. | ||
- | for DT1, **/ | + | Listed below are some instructions |
- | for DT2, **/homes/ | + | **/home/ |
- | There are key things to change in the dyn.csh file | + | There are key things to change in the dyn.csh file: |
- | 1. # number of tasks and nodes to run your job (talk to Dr. Klauda) | + | - # number of nodes to run your job (talk to Dr. Klauda) |
+ | - You should adjust the job name to something for your system. | ||
+ | - Adjust the SBATCH and namd run lines per the number of nodes (see examples in the the following directory: ~jbklauda/ | ||
+ | - Also there is a line with set simt = 1000000. This is to run 1 Million steps of 2ns per block (with 2fs timesteps). | ||
- | 2. You should | + | You then will need to adjust |
- | 3. mpirun -np command with the same number of tasks | + | Note: dyn-1.inp |
- | + | ||
- | 4. Also there is a line with set simt = 1000000. This is to run 1 Million steps of 2ns per block. | + | |
- | + | ||
- | You then will need to adjust | + | |
Once the changes are made you will also need to copy the step*6.6.xsc/ | Once the changes are made you will also need to copy the step*6.6.xsc/ |
production_run.1474388108.txt.gz · Last modified: 2016/09/20 11:15 (external edit)