[gmx-developers] Live Visualization of Simulations

David van der Spoel spoel at xray.bmc.uu.se
Thu May 22 13:56:14 CEST 2008

Martin Höfling wrote:
> Am Donnerstag, 22. Mai 2008 schrieb Mark Abraham:
>> Martin Höfling wrote:
>>> Hello again,
>>> I really would like to see some sort of visualization of running
>>> simulations. First question would be if there's anybody else working on
>>> it to bundle efforts....
>>> My thougts about it were to implement simple additional "trajectory
>>> writing" via xml-rpc to a running xml-rpc enabled pymol session (not
>>> necessarily on the same machine). This would introduce dependency of the
>>> xml-rpc C library and probably introduces some latencies (...shouldn't be
>>> used for long production runs). Do you have any other suggestions or
>>> comments about it?
>> NAMD has some capability along these lines.
> Yepp, including live feedback integrated into vmd and other nice toys. I am 
> basically only interested in monitoring short simulations and don't wanna 
> switch to NAMD for this.
> Best
> 	Martin
You can of course run ngmx on a running simulation... We used to have 
synchronization between ngmx and mdrun, but it wasn't very portable.

Long term it would be nice to have this kind of functionality.

David van der Spoel, Ph.D.
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se

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