VMD-L Mailing List

From: Dominique Vlieghe (dominique.vlieghe_at_dmbr.UGent.be)
Date: Fri May 07 2004 - 09:25:39 CDT

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
>>
>>
>
>
> 

-- 
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Dominique Vlieghe, Ph.D.,
Bioinformatics Core,
Department for Molecular Biomedical Research (DMBR)
VIB - Ghent University
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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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