[gmx-users] Re: Groups based on distance criteria

Vasilii Artyukhov darth.vasya at gmail.com
Mon Jul 20 17:39:13 CEST 2009

2009/7/20 Vitaly V. Chaban <vvchaban at gmail.com>

> Hi Matteus,
> Yeah, dynamic groups would be a powerfull tool. But such mechanism is still
> under development if I am not out-of-time.
> The possible way to proceed with such kind of research (as Berk advised me
> here long ago) is to sort the trajectory (trjorder) based on the distance
> criteria. Then you can make an index file with N first numbers (which are
> close to the protein) and use g_energy with this group and protein group. It
> seems for your task this way is a perfect solution.

Or better yet, use mdrun -rerun on your reordered trajectory and _then_ use
g_energy? This way you would be free of any problems with molecules going in
and out of your solvation shell, if I am getting things right.
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