From: John Stone (
Date: Wed Jul 18 2012 - 09:46:30 CDT

  Do you have NAMD installed on your cluster? The namdenergy plugin works
by launching NAMD. If NAMD is either unavailable or has some unexpected
problem launching on the cluster, then the namdenergy plugin would not
succeed, however I would normally expect it to emit some kind of warning
or error messages to the VMD console or to the Tk console during the attempted
run. What output does namdenergy give you when you run it?

  John Stone

On Tue, Jul 17, 2012 at 11:28:06PM -0400, Wang Yi wrote:
> Dear VMD users,
> I was trying to use the text mode of VMD to calculate complex interaction
> energies from a series of long trajectories. I decided to submit the job
> to the cluster and let it run in batch mode. But I found an interesting
> problem -- the "namdenergy" command doesn't run at all when I run the job
> remotely.
> First, I did include "package require namdenergy".
> Secondly, the same tcl script, runs perfectly when I run it on the command
> line of the login-terminal.
> Third, as long as the script is submitted to a remote computer node, VMD
> seems to have skipped namdenergy. No error message, program exited
> normally.
> Has anyone seen this kind of behavior before?
> Thanks.
> ___________________________
> Yi (Yves) Wang
> Duke University

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