[gmx-users] Snapshot taken under certain condition

Mark Abraham Mark.Abraham at anu.edu.au
Wed Oct 7 03:21:22 CEST 2009

Arik Cohen wrote:
> Dear users,
> Is there a way(in the mdp file) to take a snapshot of only the C-alpha 
> atoms along a trajectory if certain condition are met(tested every time 
> a snapshot needs to be taken) ?

If you know in advance you'll only ever want the C-alpha atoms for 
analysis (dangerous) then you can use xtc-groups to write only that set. 
Better is to savee all the data you might want, and then filter for the 
C-alpha atoms with trjconv at a suitable point.

You cannot apply your condition during the simulation, but must apply it 
after the fact. For example, use a suitable analysis tool, and then 
perhaps post-process that output to provide input to trjconv to extract 
the frames of interest. The detail of the necessary procedure will 
depend on the nature of the condition you want to apply.


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