[gmx-developers] IMD patch

[Marc Baaden]

Dear Martin Hoefling (and Gromacs developers),

We recently caught track of your email exchange on the Gromacs mailing 
list, where you contributed a patch for using IMD via Gromacs and 
raised some interesting IMD-related issues.

Recently, we have developped a very similar application aiming at
coupling calculation code (including Gromacs) to a visualisation tool
(including VMD) for a convenient and an optimal use of interactive molecular
simulations.

Our program, called MDDriver, and using an already described patch
co-developped with the Gromacs team [1-3] should be available in a few
weeks at

  http://sourceforge.net/projects/mddriver/

There are currently two main papers related to this MDDriver library, 
one in VRST 2008 and one in VRIPHYS 2008, which we can provide upon request.

There is also a preliminary Demo Movie at

  http://www.baaden.ibpc.fr/projects/mddriver/MDDriver.m4v

If you are interested in this work, we can send you a code
version and tutorial before the official release date.

Best regards,
Marc Baaden, Nicolas Ferey & Olivier Delalande.


NB: After the official release, we very much hope to convince the 
Gromacs developers to eventually include our IMD implementation in an 
upcoming future version.


[1] http://www.gromacs.org/pipermail/gmx-developers/2005-June/001130.html
[2] http://www.gromacs.org/pipermail/gmx-developers/2007-October/002267.html
[3] http://www.gromacs.org/pipermail/gmx-developers/2008-May/002567.html


martin.hoefling at gmx.de said:
>> Hello Gromacs Developers,
>> here's my first version of a patch, implementing the IMD =
>> Interactive  Molecular Dynamics Protocol into recent Gromacs CVS
>> versions.

>> Currently, the following works, at least here: -Connecting via VMD to
>> a running single or MPI simulation with md integrator. -Updating the
>> coordinate/energy to vmd and set update frequency from vmd.
>> -Detaching and reattaching from/to a running simulation. -Reading and
>> printing out new forces from VMD (pretty useless atm).

>> When you've compiled a mdrun binary, you can run it with -imd switch.
>> In VMD,  you need to load the corresponding structure and then
>> connect to gromacs via  Extensions->Simulation->IMD Connect (NAMD)

>> ToDo & Questions:

>> - My current implementation syncronizes IMD (e.g. output frequency)
>> only on  next IMD output, to reduce communication. Is this ok? My
>> idea would be to  implement the force synchronization from master to
>> other processes here as  well.

>> -Implement action of VMD forces. VMD sends new forces, applied via
>> mouse to  the master. The simplest idea would be to create a local
>> list with all added,  changed and deleted forces and communicate this
>> list to all processes as  mentined above. Then I need to find out how/
>> where to implement the force  update per process.

>> -PBC treatment, currently molecules look not so nice after crossing
>> the  boundaries.

>> -Allow only a certain group to be send to VMD, maybe write out a
>> matching  structure for IMD-client as well.

>> -Implement IMD into other integrators.

>> -MPI_Bcast crashes If only one MPI process... ... is (cr->nnodes > 1)
>> the proper condition?

>> -Energies displayed in VMD might be wrong, conversion should be OK
>> but I  didn't really think about if the contributions are correct.

>> OK, any comments, suggestions,...	 ;-)

>> ...I am sure there's a lot of stuff one can do better.

>> Cheers,
>> 	Martin 



  Marc Baaden


-- 
 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