AMBER Archive (2008)

Subject: Re: AMBER: B-factor calculation from data with different write frequencies

From: Bill Ross (ross_at_cgl.ucsf.edu)
Date: Wed May 28 2008 - 13:11:30 CDT

> The value of the B-factor CANNOT depend on your sampling frequency !

Thanks, Adrian.

> B-factors (related to RMSF but not quite) are thermodynamic properties,
> so as long as their value is converged, it could not possibly matter how
> often you saved frames.
>
> Sampling for convergence is of course really hard to do, but in regular
> MD it depends only on how long you run.

So theoretically a uniform sampling of the two runs (equivalent to
ntwx=500) should give about the same result as the concatenation of
ntwx=100 and ntwx=250 runs.

> So, if you believe you have run long enough, you can directly compare
> RMSF or B-factors for two different simulations with different ntwx
> without any need for downsampling.

How does one decide what is long enough? Is there a heuristic, other
than "as long as one can afford"?

Bill

>
> I hope this helps !
>
> Adrian
>
>
> Bill Ross wrote:
> >> but will I be sacrificing "quality" of the B-factor
> >> calculation due to reduced MD sampling?
> >
> > I imagine so, but I'm not an expert on this. Maybe someone else can
> > comment on how significant a difference the sampling difference makes.
> > The alternative is to re-run one of your calculations, or possibly
> > continue your ntwx=250 calculation.
> >
> >> Also, I have conducted an
> >> independent simulation of the same molecule with no ligand bound
> >> (first simulations were with bound ligand) and with ntwx = 250. Will
> >> I need to select every other frame from this trajectory as well, in
> >> order to make the data sets comparable?
> >
> > Yes, or just compare to the ntwx=250 part of the ligand run. I.e. stage 1
> > would be compare the ntwx=500 (selected/aggregated) joint run to the
> > ntwx=250 portion of the ligand run, then if they agree, compare 250 to 250
> > ligand/non-ligand.
> >
> > Bill
> > -----------------------------------------------------------------------
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>
> --
> Dr. Adrian E. Roitberg
> Associate Professor
> Quantum Theory Project
> Department of Chemistry
>
> Senior Editor. Journal of Physical Chemistry
> American Chemical Society
>
> University of Florida PHONE 352 392-6972
> P.O. Box 118435 FAX 352 392-8722
> Gainesville, FL 32611-8435 Email adrian_at_qtp.ufl.edu
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