AMBER Archive (2008)

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

From: Adrian Roitberg (
Date: Wed May 28 2008 - 13:58:53 CDT

>> 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.

Dear Bill,

Indeed, you should get the same answers in the limit of a long run. You
do not even need uniform sampling ! You just need proper Boltzmann
sampling, intrinsic to properly run MD.

>> 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"?

Ah !!! THE question...

If anyone knows, please answer to the list !.

Short answer: no one knows how long is long enough. You must look at
trends vs time (B-factors every 10 ps), or cumulative values vs time.
Better yet, you can run two independent simulations from different
initial conformations and velocities and see if your two runs give you
similar values. There is no easy answer, but one MUST look and at least
attempt to ask if what you have done so far 'looks' like good enough.


                            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