AMBER Archive (2008)

Subject: Re: AMBER: atomic posiltional fluctuation

From: Thomas Cheatham III (tec3_at_utah.edu)
Date: Tue Apr 01 2008 - 11:50:43 CDT


> I calculated atomic positional fluctuations of my Molecular Dynamic
> Simulation with AMBER 9.0.
> I would like to know if the results are the mean of the squared
> fluctuations [x=(ax+bx+cx)/3] or the sum of their components (x =
> ax+bx+cx).
> What the equation which is used by the command atomicfluct?

Both; if you specify the "bfactor" keyword, than the results reported are

  (8/3)*pi**2 * r**2 where r**2 = (x**2 + y**2 + z**2)

If "bfactor" is not present, then the raw fluctuation is reported,

  r = sqrt(x**2 + y**2 + z**2)

"bfactor" provides the mean (through the 1/3); no "bfactor" produces the
sum (but the sqrt of r**2). The easiest way to understand this is to look
at the code (actions.c, transformAtomicFluct() and trust the code rather
than the comments) or to try to decipher past notes in the e-mail
reflector.

-- tec3
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