Klauda Lab Simulation Wiki

This page is read only. You can view the source, but not change it. Ask your administrator if you think this is wrong.
====== Rest2 ======

Copy rest2 folder from the following directory into the CHARMM folder:


///homes/jbklauda/sim-inputs/rest2//

**input/output/toppar:**
  * Create ‘toppar’ folder and copy the toppar files within the namd directory and paste them into this new folder
  * Create directories in the ‘output’ folder labeled 0 to [# of replicas – 1] (Ex: if you’re designing 10 replicas, make 10 folders labeled 0-9)
  * Delete the files in ‘input’. Unzip and copy dyn1.coor/xsc/vel and rename these files to equinpt.coor/xsc/vel
**dyn.csh:**
  * Change ntasks, nodes, and job name as appropriate (talk to advisor for this)
  * Change the bolded parts in the following line as appropriate

mpirun -machinefile $PBS_NODEFILE -np **300** $namddir/namd2 +replicas **30** job16.conf +stdout output/%d/job16.%d.log

**makefile.csh:**
  * Change the bolded parts in the following line as appropriate

echo "mpirun -machinefile ${str}PBS_NODEFILE -np **300** ${str}namddir/namd2 +replicas **30** job$j.conf +stdout output/%d/job$j

**rest2.conf:**
  * Change num_replicas to the number of replicas for system
  * Change min and max temp to the correct temperatures
    (Talk to advisor for these values if unsure)
    
**rest2_base.namd:**
  * Make the following change to the first two lines:

../step3_pbcsetup.xplor.ext.psf

../step3_pbcsetup.pdb

  * Make sure the file inputs match all inputs and parameters from step5_production.inp input file
  * Go to bottom and change the sptFile to the name of the .pdb file you created with the beta1 column and add ‘../’ to the beginning like at the top

**top.txt:**
  * Change the ntasks, nodes, and job name as appropriate

Now you’re ready to run.
Type:
     chmod u+x dyn.scr
     ./dyn.scr