On Thu, Nov 15, 2012 at 7:55 PM, Sajeewa Pemasinghe <sajeewasp.gmail.com>wrote:
> Hi all,
>
> In my MD simulation I have specified a bellymask in which I want
>
> "All the atoms within 80 angstroms of the residue 324 to move except for
> the residues 999-1039".
>
> So the way I have specified it is
>
> ibelly=1,bellymask= '(:324 <.80.0) & !(:999-1039)',
>
Masks do not update their selection as the simulation progresses.
Therefore, if something diffuses away, it will not be 'removed' from this
belly mask.
Also note if this is an explicit solvent simulation, you might be seeing
the periodic image of something that is otherwise much closer.
Good luck,
Jason
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Thu Nov 15 2012 - 18:30:01 PST
