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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> > 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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>
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Received on Tue Aug 31 2010 - 07:00:06 PDT
