Klauda Lab Simulation Wiki

Listed below are some instructions for the production run simulation on DT1/DT2 (slight differences for MARCC). As we discussed, this will automatically run your simulation in chunks with each being a certain length. The files to copy (not the sub-directories) are in the following location on DT1/DT2 to your directory with step6.1 to step6.6 namd files:

for DT1, /homes/jbklauda/sim-inputs/namd/npt-membrane

for DT2, /homes/jbklauda/sim-inputs/namd

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)
2. You should adjust the job name to something for your system.
3. mpirun -np command with the same number of tasks
4. Also there is a line with set simt = 1000000. This is to run 1 Million steps of 2ns per block (with 2fs timesteps). Discuss with Dr. Klauda and/or a graduate student on what to change this to and also change in the dyn-2.inp file.

You then will need to adjust dyn-1.inp and dyn-2.inp to match with what step7_production.inp has. This file will be combined into a dyn.inp file with the firsttimestep defined (see dyn.csh file). One key important change could be the final line in dyn-2.inp. This should be set to the simt value.

Once the changes are made you will also need to copy the step*6.6.xsc/.vel/.coor to dyn.xsc/vel/coor so the job will use these to restart from your equilibration runs. Then to run the production run, just type:

 ./dyn.scr 

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.