[gmx-developers] Live Visualization of Simulations

[David van der Spoel]

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