AMBER Archive (2004)

Subject: Re: AMBER: atomicfluct in ptraj

From: Holger Gohlke (
Date: Wed Apr 14 2004 - 14:14:47 CDT

Qiang Lu schrieb:
> Dear all,
> I have a question about the command atomicfluct in ptraj. Does it
> align the structure before the calculation of atomic fluctuation?

No, it doesn't.

> What if the whole protein has a movement or rotation during the
> simulation.

You need to align the snapshots to a reference prior to calculating the
fluctuations (see the "rms" command in the ptraj documentation).

Best regards


!!!      Please note new telephone number      !!!
Dr. Holger Gohlke

J.W. Goethe-Universität Fachbereich Biologie und Informatik Institut für Mikrobiologie Marie-Curie-Str. 9 60439 Frankfurt/Main Germany

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