multiple automated calls to NAMD

Date: Wed Jun 08 2005 - 20:57:56 CDT

Hello everyone:

I posted on this topic (to NAMD-L only) a month ago, but heard no response,
so I'll try again...

I have need for running NAMD multiple times (for short minimization runs)
in a semi-automated way, driven by a VMD (Tcl) script. My inquiry is this:

Is it possible to send command-line parameters to NAMD? Something
analogous to the "args" command for VMD or 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, and this works if I set the variables from
my C-shell and run NAMD once; but when I tried this using "exec setenv"
commands from within a VMD/Tcl script, the environment variables were not
readable by NAMD. I also tried reading/writing my variables from/to a text
file, using Tcl commands from within VMD and NAMD, but again to no avail.
(Again, running my NAMD job directly from the Unix shell, taking its input
parameters from my VMD-written text file, DOES work; but this time, when I
try running the same NAMD config file from within VMD, I get this message:
"ERROR:src/NamdState.C(158): Number of pdb and psf atoms are not the same".)

I had hoped that, since NAMD and VMD come from the same "house" and are
supposed to play well together, that there might be a simple solution to
my problem. Maybe I've just missed something obvious? Well, anyone who
has any experience and could shed some light, I'd be most grateful.

thanks, as always,
- Erik

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

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