> I am using ptraj (Amber 9) for analyzing the trajectory obtained after
> simulation of 1ns of an RNA pseudoknot. Can you please tell me the
> difference in the functionalities of rms and atomicfluct command. What
> reference does atomicfluct uses for calculating positional fluctuations? Is
> it some structure or is it calculated over time.
atomicfluct uses the current reference frame (or equivalently does not set
up a reference frame). To calculate atomicfluct (or B-factors) as we
would normally want to calculate them (i.e. removing rotation/translation
and fitting to a common reference frame) you would first calculate an
average structure, rms fit to this average structure, and then run
atomicfluct. This requires two-passes through the data, once to create
the average structure (which also requires an RMS fit to a common
reference frame) and another run to do the fit/atomicfluct.
If you want approximate fluctuations, you can fit to the first frame, and
get the results in a single ptraj run:
rms first mass :1-999
atomicfluct out apf-byres.dat :1-999 byres
--tec3
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Received on Tue Nov 29 2011 - 10:00:04 PST
