Thanks allot for all your help
Arik
Mark Abraham wrote:
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.
Mark
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