AMBER Archive (2009)

Subject: Re: [AMBER] how to calculate correct RMSF?

From: case (
Date: Mon Sep 14 2009 - 07:33:29 CDT

On Mon, Sep 14, 2009, Catein Catherine wrote:
> Could you mind to the unit of the results?

Amber reports lengths (such as a root-mean-square fluctuation) in Ang.

> RMSF=(value in xxx.apf * 3) / (8 * pi * pi)

This is not correct. You should replace "value in xxx.apf" above by its square
root. But why not just leave out the "bfactor" keyword and see what you get?


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