Thank you very much Jason!
> Date: Tue, 7 Apr 2015 14:41:36 -0400
> From: jason.swails.gmail.com
> To: amber.ambermd.org
> Subject: Re: [AMBER] Boltzman Weights from MD trajectory
>
> On Tue, Apr 7, 2015 at 2:33 PM, Emilio Angelina <
> emilioluisangelina.hotmail.com> wrote:
>
> > Hi,
> >
> > I would like to compute some properties derived from charge density on one
> > or more snapshots from molecular dynamics trajectories by performing QM
> > calculations.
> > Since computing these properties on a single structure might be
> > meaningless, I was thinking in performing a clustering analysis using
> > ptraj, pick a representative structure from each cluster and compute the QM
> > properties on each of those representative structures.
> > Then, my problem is how to combine the QM results from all the snapshots
> > to get a single result, for example a single interaction energy that then I
> > can compare with binding affinity experimental data.
> > Would it be possible to weight the results from each representative
> > structure by its Boltzman weight?
> > Or should I just average the results?
> > I know that the best way of taking into account the Boltzman distribution
> > would be to take a very large number of independent snapshots from
> > trajectory just like in MM-PBSA but, since the QM calulations are too
> > expensive I only can take a small number of frames, so I would need a way
> > to explicitly compute the Boltzman weights.
> >
>
> I would do a weighted average by the cluster populations (which should,
> themselves, be Boltzmann-weighted by virtue of running a MD or proper MC
> simulation).
>
> So the average I would do would be something like this:
>
> <A> = SUM_x( Nx * A(X) ) / Ntot
>
> where the summation runs over all clusters (x), X is the centroid of
> cluster x, Nx is the number of points in cluster x, and Ntot is the total
> number of points in the trajectory.
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Apr 07 2015 - 13:30:04 PDT
