Hello,
How are you constructing the PMF? Are you using SMD and calculating the PMF
with the Jarzynski equation? Are you using umbrella sampling? If you are
using SMD with Jarzynski averaging, you should include every single
trajectory in your average to get the total PMF. You can find likely the
"best" pathway, or the one that corresponds closest to the PMF, by comparing
the potential energy surface of each simulation with the average PMF
obtained from averaging all of them, and whichever one follows that curve
closest will probably be a good choice.
Hope this helps,
Jason
On Tue, Aug 17, 2010 at 7:00 AM, Catein Catherine <askamber23.hotmail.com>wrote:
>
> Dear All,
>
>
>
> I would like to stuy the drug dissociation pathway from a receptor.
>
>
>
> I tried to use PMF to discript the distance between the drug and the active
> site. I noted that the path is sensitive to the atoms used to define the
> distance restraint.
>
>
>
> If I want to chose the most important drug dissociation pathway for further
> discussion, is the one with the lowestest energy should be used? If not,
> what is the requirement should be used to chose the right pathway?
>
>
>
> best regards,
>
>
>
> Cat
>
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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 17 2010 - 06:00:09 PDT
