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:
echo “mpirun -machinefile ${str}PBS_NODEFILE -np 300 ${str}namddir/namd2 +replicas 30 job$j.conf +stdout output/%d/job$j
rest2.conf:
(Talk to advisor for these values if unsure)
rest2_base.namd:
../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:
Now you’re ready to run.
Type:
chmod u+x dyn.scr
./dyn.scr