VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri May 07 2004 - 09:30:26 CDT

Dominique,
  I have no plans to work on energy evaluation tools personally,
I already have a long list of work to do on core parts of VMD.
As you point out, Jan and others have come up with plugin-based
solutions to calculate these values. Besides Jan's technique, there's
also a method that requires running NAMD for one timestep, though I'm
not as familiar with that method. I suggest you direct your inquiries
to Jim Phillips, as he is familiar with the licensing issue that Jan Saam
mentioned, and would also know how to do the alternative method using NAMD.

Thanks,
  John Stone
  vmd_at_ks.uiuc.edu

On Fri, May 07, 2004 at 04:25:39PM +0200, Dominique Vlieghe wrote:
> Hi,
>
> I was the person who asked the similar question. I got a nice reply of
> Jan Saam from Germany saying he had made such a tool and that he had
> given it to John, but there were some licensing issues so that the tool
> was not published at that time.
>
> So John, I guess the question remains: will there be such a tool
> available for VMD? I think this would be wonderful, because it would
> change VMD from a visualisation tool to a analysis tool, which sounds
> great...sorta
>
> Regards
>
> D
>
> John Stone wrote:
>
> >Hi,
> > The 'potential' and other energy values queryable within VMD are
> >intended for use with IMD simulations where VMD receives energy information
> >from NAMD as the simulation runs. This feature allows tools such as the
> >IMD menu plugin to display energies as VMD receives data from a running
> >simulation.
> >In general however, most structure and trajectory file formats don't
> >provide this information, so these values are set to zero when not
> >performing
> >an interactive MD simulation.
> >
> >Thanks,
> > John Stone
> > vmd_at_ks.uiuc.edu
> >
> >On Thu, May 06, 2004 at 12:28:49AM -0400, Shirley Hui wrote:
> >
> >
> >>I was wondering if anyone knew if it is possible to calculate potential
> >>energy of a molecule that is loaded into VMD.
> >>I read the User Guide and noticed that molinfo has a get command called
> >>potential which is the total potential energy.
> >>http://www.ks.uiuc.edu/Research/vmd/current/ug/node125.html
> >>I tried using this. I loaded a pdb file into VMD. Then I ran the command
> >>(where 1 is the mol id of the molecule): vmd > molinfo 1 get potential
> >>0.000000
> >>But I alwasy get 0.00000 as the energy. I don't believe this is correct.
> >>What am I missing??
> >>I noticed on the mailing list someone posted a similar message about
> >>calculating potential energy, someone replied saying they had a script to
> >>do it, but they never posted it?
> >>http://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/1643.html
> >>Can anyone provide some insight???
> >>>From my look at the mailing list I don't think VMD is capable of
> >>>calculating energies. But then my question is why allow such a feature
> >>>in the molinfo command???
> >>Thanks,
> >>shirley
> >>
> >>
> >
> >
> >
>
>
> --
> -----------------------------
> Save the Hubble petition: http://www.savethehubble.org
> ------------------------------
> Dominique Vlieghe, Ph.D.,
> Bioinformatics Core,
> Department for Molecular Biomedical Research (DMBR)
> VIB - Ghent University
> 'Fiers-Schell-Van Montagu' building
> Technologiepark 927
> B-9052 Ghent (Zwijnaarde), Belgium
>
> Tel : +32-(0)9-33-13.693
> Fax : +32-(0)9-33-13.609
> email:dominique.vlieghe_at_dmbr.ugent.be
> www:http://www.dmbr.ugent.be/
> ------------------------------ 

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