[gmx-users] Snapshot taken under certain condition

[Arik Cohen]

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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