VMD-L Mailing List

From: Shirley Hui (shirleyhui_at_alumni.uwaterloo.ca)
Date: Fri May 07 2004 - 09:44:04 CDT

VMD is already capable of providing some level of analysis in that is able
to calculate RMSD values between structures etc (i.e. through the tcl
command or RMSD calculator), so it's not just a visualization tool. RMSD is
good if you are only interested in how similar two structures are
geometrically. But it doesn't give you an idea of how feasible the
structure is. An energy value would provide a better indication of this.
NAMD is capable of calculating these energy values I believe, but for the
most part it seems like alot of overhead to set it up just for a few
calculations?? Correct me if I am wrong as I have only read about or looked
into this and not tried it out myself.
As a result, I am also looking into other packages like MMTK that are not
visualization tools, but do provide means to calculate energy values in a
much more straightforward manner and can be plugged more "seamlessly" into
applications like Pymol.
I think energy calculations would be a great feature too add on to VMD as
most free visualization tools (that I know of) don't provide this kind of
analysis.
It would certainly put it up and above other free applications out there if
this functionality was available.
Thank you,
shirley

----- Original Message -----
From: "Dominique Vlieghe" <dominique.vlieghe_at_dmbr.ugent.be>
To: "John Stone" <johns_at_ks.uiuc.edu>
Cc: "Shirley Hui" <shirleyhui_at_alumni.uwaterloo.ca>; <vmd-l_at_ks.uiuc.edu>
Sent: Friday, May 07, 2004 10:25 AM
Subject: Re: vmd-l: VMD: Potential Energy Calculation

> 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/
> ------------------------------
>
>