From: Leandro Martínez (
Date: Tue May 22 2007 - 20:57:01 CDT

The article

Unbinding of Retinoic Acid from its Receptor Studied by Steered
Molecular Dynamics
D Kosztin, S Izrailev, K Schulten - Biophysical Journal, 1999

Does that and provides a formulae. It is a simple operation with the
atomic fluctuations ( 8/3 pi^2 <rmsd> ) if I remember correctly.
That is not the main reference for that, but maybe you can find
further references there.


On 5/22/07, <> wrote:
> Hello,
> I am currently running simulations in NAMD, and would like to calculate
> b-factors (temperature factors) from my .dcd files in order to compare
> them to observed values from x-ray crystallography. I have tried
> searching extensively through the submitted scripts and emails, and
> could not find a suitable answer for how to perform this calculation.
> In the past I used the AMBER software, and it had a built-in b-factor
> command, so I assume such a calculation can be performed reasonably in
> VMD/NAMD. Any suggestions will be welcome.
> Thank you,
> Gabriel Ozorowski
> Department of Molecular Biology & Biochemistry
> University of California, Irvine
> Steinhaus Hall 540
> Irvine, CA 92697-3900