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