production_run
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| - | Here are production run instructions for DT1/DT2. | + | [[bilayer_simulations]] |
| - | 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. | + | ==== Production run instructions for Zaratan ==== |
| - | for DT1, **/ | ||
| - | for DT2, **/ | + | Listed below are some instructions |
| + | **/ | ||
| - | 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) | + | There are key things |
| - | 2. You should adjust the job name to something for your system. | + | - # 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). | ||
| - | 3. mpirun | + | You then will need to adjust dyn-1.inp and dyn-2.inp to match with what step7_production.inp has. These files will be combined into a dyn.inp file with the firsttimestep defined (see dyn.csh file). The easiest way to do this is to copy and paste the psf/pdb lines in step7*inp to replace that in dyn-1.inp. Then, copy most of the step7*inp to replace the material in dyn-2.inp. One key important change will likely be the values for the " |
| - | 4. Also there is a line with set simt = 1000000. This is to run 1 Million steps of 2ns per block. | + | Note: dyn-1.inp |
| - | + | ||
| - | 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/ | ||
| - | **./dyn.scr** | + | <code commend> |
| Also note that there is an important file (last.seqno). This tells the daisy-chain script when to stop. So if you want to run for a total of 100ns you'll need 50 files so this is the value that should be in the last.seqno file. If you want this to be longer or short just change the number in the file. | Also note that there is an important file (last.seqno). This tells the daisy-chain script when to stop. So if you want to run for a total of 100ns you'll need 50 files so this is the value that should be in the last.seqno file. If you want this to be longer or short just change the number in the file. | ||
production_run.1472411100.txt.gz · Last modified: 2016/08/28 14:05 (external edit)