VMD-L Mailing List

From: Justin Gullingsrud (jgulling_at_mccammon.ucsd.edu)
Date: Fri May 07 2004 - 12:49:37 CDT

Just wanted to point out that, from VMD's Python interface, you can also
type "from MMTK import *" and mix and match VMD's and MMTK's python
commands as much as you'd like. VMD also provides commands for
accessing and modifying timesteps efficiently using Numeric arrays.
I've actually started using MMTK a bit for my own work so I might more
suggestions along these lines as things progress.

Cheers,
Justin

On Fri, May 07, 2004 at 10:44:04AM -0400, Shirley Hui wrote:
> 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/
> > ------------------------------
> >
> > 

-- 
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