Thank you very much Jason. The fact that "masks do not update as the
simulation progresses" really solved my problem.
Sajeewa
On Thu, Nov 15, 2012 at 9:18 PM, Jason Swails <jason.swails.gmail.com>wrote:
> 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
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Nov 15 2012 - 20:00:02 PST
