[gmx-developers] real-time GROMACS visualization

David van der Spoel spoel at xray.bmc.uu.se
Thu Jun 16 09:22:24 CEST 2005

On Thu, 2005-06-16 at 07:17 +0200, Marc Baaden wrote:
> Dear Simon,
> we are working on a general framework for interfacing simulation codes
> with VMD in order to do real-time control but also interaction. You have
> probably seen the "Sample IMD protocol and API implementation for use
> in simulation programs" on the page [1], which I contributed to VMD some
> time ago at an early stage of our project. Meanwhile we have made some
> progress towards a general interface written as a shared library.
> We have so far mainly interfaced our in-house code with VMD, which works
> fine (for C, C++ and fortran). From that experience I can tell that if
> you want to interface Gromacs just for visualization, this will be a piece
> of cake. Concerning interaction with the simulation, this is a much harder
> job. As far as I know nobody else has done this (for Gromacs) nor is working
> on it.
> So if you were going to work on this at ClearSpeed, this might be very
> helpful for the community - depending on how the resulting code would be
> released - as what we(*) are most lacking is not ideas but gifted programmers.

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...

David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,          75124 Uppsala, Sweden
phone:  46 18 471 4205          fax: 46 18 511 755
spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel

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