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
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Received on Tue Aug 31 2010 - 07:00:02 PDT
