Run NAMD in loops

From: Neelanjana Sengupta (
Date: Sun Apr 22 2007 - 05:36:33 CDT

Hello NAMD folks,

For a dipeptide, I need to find the different energies as a function of the
dihedral angles (phi, psi). For this, I need to set the angles (through
application of restraints), and then run short minimization at each (phi,
psi) combination...

Can you please tell me how to how to run NAMD inside loops? Essentially, I
want to be able to achieve something like this:

for {phi = -180 to 180, incr by 20} {
           for {psi = -180 to 180, incr by 20} {

                   specify restraint with (phi, psi)
                   run minimization
                   print output

Thanks and regards,

Neelanjana Sengupta, PhD student
Dept. of Chemistry
Univ. of California-Irvine
Irvine, CA 92697
Phone: 1-949-824 9921

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