[gmx-developers] real-time GROMACS visualization

Marc Baaden baaden at smplinux.de
Thu Jun 16 09:36:00 CEST 2005

>>> David van der Spoel said:
 >> Actually we are working on a GUI for gromacs based on Qt. This will make
 >> it portable to Linux/Mac/Windows (from Qt version 4.0). It uses PyMOL
 >> for visualization.
 >> It is not meant to be a real-time thing, but you can change some
 >> parameters and do a quick simulation. I know that VMD has stuff like
 >> pulling on atoms and see the response, and although that can be
 >> instructive, it is not clear to me what the scientific value of that is,
 >> although I may be ignorant...

I would argue - but time will show - that this is comparable to visualization,
eg is it only informative or does it add scientific value ? I'd guess that
crystallographers might advocate the scientific value of vis. What I mean is
that in principle everything you can visualize is the same information as just
printing out the corresponding PDB file, but for a human it is more intuitive
to have a nice picture on the screen.
The same might go for interactive simulations, in principle everything is
doable by sound, long, non-interactive, classical (as in "as we used to do
for the last 20 years") MD simulations, but it takes time and considerable
effort for the analysis. I don't say this is to be replaced by interactive
stuff, but I could see a lot of benefit in deciding about details *before*
launching months of number-crunching jobs on the basis of some interactive
In the best case scenario an interactive exploration would already show a
rough feature that could then be confirmed and analysed in detail in a
full MD simulation. This will depend on how subtle/robust the feature is
against approximations and simplifications which are obviously needed for
the interactive approach.

Do I have a point ?


 BioMolSim meeting 2&3 Sep 2005: http://www.iecb.u-bordeaux.fr/satellite2005/

 Dr. Marc Baaden  - Institut de Biologie Physico-Chimique, Paris
 mailto:baaden at smplinux.de      -      http://www.baaden.ibpc.fr
 FAX: +33 15841 5026  -  Tel: +33 15841 5176  ou  +33 609 843217

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