AMBER Archive (2002)

Subject: Re: atomicfluct in ptraj

From: David A. Case (case_at_scripps.edu)
Date: Thu Dec 19 2002 - 11:28:43 CST

On Wed, Dec 18, 2002, Kristina Furse wrote:
>
> Had a question about the calculation of atomic fluctuation in ptraj. I
> wanted to compare the Bfactors for the CA's of my protein in 50ps subsets of
> a 300ps trajectory to each other and to Bfactors calculated for the whole
> traj, as one indication that the system is equilibrating. When I did this,
> the resulting Bfactors for the enitire 300ps run were larger than the
> average of the 6 subsets. Does this sound right? Can the whole thing be more
> than the avererage of its parts? Would this possibly reflect some kind of
> net movement?

This is indeed to be expected, and reflects both the fact that it takes a
finite time for fluctuations to "build up", and (in most cases) the fact that
there can be a slow overall "drift" in the mean structure. Especially for so
short a simulation, what you report is not unexpected. (Without knowing the
actual numbers, or how much bigger they are for 300 ps than for 50 ps, I can't
say much more.)

..good luck...dac 

-- 

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David A. Case                     |  e-mail:      case_at_scripps.edu
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