AMBER Archive (2008)

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

From: Adrian Roitberg (
Date: Wed May 28 2008 - 12:54:09 CDT

Hi all,

I am trying to figure out exactly what the underlying issue here is, but
let's make something clear first.

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

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, 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.

I hope this helps !


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 ----------------------------------------------------------------------- The AMBER Mail Reflector To post, send mail to To unsubscribe, send "unsubscribe amber" (in the *body* of the email) to