NAMD automation

Date: Sat May 07 2005 - 23:39:16 CDT

Hi folks,

I have need for running NAMD multiple times (for short minimization runs)
in a semi-automated way, driven by a wrapper script. Thus, two questions:

1) Is it possible to send command-line parameters to NAMD? Something
analogous to the "args" command for simple Tcl procs? If not, how can I
communicate the values of variable parameters from a higher-level script
into a particular instance of NAMD? I see in the manual that NAMD can
read shell environment variables, so this was the route I was going to try
first, but perhaps there is a more elegant method?

2) When doing minimization in NAMD, is there some way to insert a test for
convergence? That is, rather than having the run always go for the
prescribed number of steps, can NAMD check the value of the gradient (or
something else) and exit early if some condition is met? (I recall someone
else asking a similar question not long ago, but don't recall seeing any
answer... apologies if I missed it.)

thanks much,
- Erik

C. Erik Nordgren, Ph.D.
Department of Chemistry
University of Pennsylvania

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