Differences

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--- production_run [2021/06/07 09:05] – admin
+++ production_run [2022/09/28 17:23] (current) – admin
@@ Line 1: / Line 1: @@
 [[bilayer_simulations]]
-==== Production run instructions for DT2 ====
+==== Production run instructions for Zaratan ====
-Listed below are some instructions for the production run simulation on 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 DT2 to your directory with step6.1 to step6.6 namd files:
+Listed below are some instructions for the production run simulation on Zaratan. 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 Zaratan to your directory with step6.1 to step6.6 namd files:
-for DT2, **/homes/jbklauda/sim-inputs/namd**
+**/home/jbklauda/sim-inputs/namd**
@@ Line 16: / Line 16: @@
   - 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. 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 past 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 run and numsteps lines in dyn-2.inp based on how many ns per dyn file. These should be set to the simt value.
+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 "run" and "numsteps" lines in dyn-2.inp based on how many ns per dyn file. These should be set to the simt value.
 Note: dyn-1.inp inputname should stay as dyn