[gmx-developers] real-time GROMACS visualization

Marc Baaden baaden at smplinux.de
Thu Jun 16 07:17:55 CEST 2005

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.

I hope this helps,


[1] http://www.ks.uiuc.edu/Research/vmd/imd/
(*) This is just a personal comment and view. Nobody take offence please.

 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

>>> "Simon McIntosh-Smith" said:
 >> Has anyone ever put together a real-time, possibly even interactive
 >> visualization of GROMACS before? I've come across a package called
 >> VMD that does this for NAMD, CHARMM etc. It comes with an API that
 >> we could wire in to GROMACS - see:
 >> http://www.ks.uiuc.edu/Research/vmd/
 >> http://www.ks.uiuc.edu/Research/vmd/imd/
 >> http://mccammon.ucsd.edu/ied/
 >> I'm interested because at ClearSpeed we've been porting GROMACS
 >> to our accelerator cards and we're at the point where we'd like
 >> to demo it running fast in real-time.
 >> If no-one's done this, and others of you think this would be
 >> a good idea, ClearSpeed might be interested in doing this in
 >> the future.
 >> Thanks for any input,
 >> Simon
 >> --
 >> Simon McIntosh-Smith, Director of Architecture & Applications
 >> ClearSpeed technology plc, www.clearspeed.com
 >> tel: +44 117 317 2132, fax: +44 117 317 2002

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