Correct (since for "ordinary" MD, you can only run MD or not run MD).
Running multiple seeds, like you did, is a good way to continue sampling
even if one simulation finds itself trapped.
All the best,
Jason
On Tue, Aug 31, 2010 at 9:44 AM, Jorgen Simonsen <jorgen589.gmail.com>wrote:
> true that would be a way to solve the problem but with "ordinary" MD only
> more sampling would solve the problem I presume.
>
> On Tue, Aug 31, 2010 at 3:30 PM, Jason Swails <jason.swails.gmail.com
> >wrote:
>
> > You could try some advanced sampling techniques like REMD or the NCSU
> > "adaptively biased MD" methods described in the amber manual.
> >
> > Good luck!
> > Jason
> >
> > On Tue, Aug 31, 2010 at 9:27 AM, Jorgen Simonsen <jorgen589.gmail.com
> > >wrote:
> >
> > > Hi all,
> > >
> > > I have started three MD simulations with different initial conditions
> in
> > > order to explore as much as possible - the problem is that one of the
> > > simulations stays in the same conformation during the whole 20 ns
> > > simulation
> > > - so one could be happy and think that it converged to the most stable
> > > structure but when I compare with the other two simulations it more
> seems
> > > that it has been "trapped" in some stable minimum - so how to treat
> this?
> > > Sample more but how much more - I would presume that I would need some
> > more
> > > sampling but one could also be "unlucky" and stay in a local minimum
> for
> > > long time.
> > > _______________________________________________
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> > >
> >
> >
> >
> > --
> > Jason M. Swails
> > Quantum Theory Project,
> > University of Florida
> > Ph.D. Graduate Student
> > 352-392-4032
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> _______________________________________________
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> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Tue Aug 31 2010 - 07:00:07 PDT
