Re: vmd-l: namdenergy plugin

From: Peter Freddolino (
Date: Mon Jul 10 2006 - 00:02:33 CDT

Hi Chandra,
this certainly does seem odd. If you don't mind, could you please send
me your psf and a couple of sample DCD frames?

By the way, just in the interests of not cross-posting too much (since
this has come up a couple times recently), can I suggested that
NAMDenergy discussion go by default to VMD-L? The NAMD features being
used here are pretty solid, so I think it's rare that NAMD-L needs to be
invoked in such a discussion (unless the question is regarding the
method for doing pair calculations itself, rather than the namdenergy
interface for it).


Chandra Ramananjara wrote:
> Hi all,
> I am having some trouble with the namdenergy plugin. I am using the
> text interface (called using the command 'vmd -dispdev text' ) of VMD
> 1.8.4 (2006-04-16) which is the latest version of VMD. I issue the
> 'package require namdenergy' command and load a psf and dcd file with
> 11 frames. I select the two groups of atoms whose interaction energies
> I am interested in calculating and then run namdenergy. I notice
> namdenergy only does the energy calculation for the first frame. The
> energies for subsequent frames are all 0, which is wrong. Also, it
> lists 12 frames, which is strange. My dcd file has only 11. Any
> suggestions as to what the problem might be ? Has anyone tried to run
> namdenergy using the text interface of the latest version of VMD ?
> Thanks,
> Chandra
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