VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu May 06 2004 - 10:15:39 CDT

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 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
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