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--- rest2 [2017/11/02 12:05] – created admin
+++ rest2 [2017/11/06 23:52] (current) – edit
@@ Line 1: / Line 1: @@
-Test
+====== 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