[gmx-developers] Live Visualization of Simulations

Mark Abraham Mark.Abraham at anu.edu.au
Thu May 22 14:04:28 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.

Sounds like adding a flush onto trajectory writes and writing a custom 
plugin for VMD/pymol/whatever that updates the current display when the 
file timestamp changes should be simple and good enough for your 
purpose... You'd want to be sure that the extra I/O burden was 
worthwhile - be that a buffered file-system write or your xml-rpc idea.


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