Thank you Jason,
How about if I was doing this with umbrella sampling?
Can I identify the most important drug dissociation pathway using umbrella sampling? When I find different results since I used different atoms to define the distance restraint?
Best regards with thanks,
Catherine.
> Date: Tue, 17 Aug 2010 08:56:29 -0400
> From: jason.swails.gmail.com
> To: amber.ambermd.org
> Subject: Re: [AMBER] How to find the most important drug dissociation pathway theoretically? PMF?
>
> 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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> > AMBER.ambermd.org
> > 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 17 2010 - 09:00:04 PDT
