Re: [AMBER] RMS fit

From: Daniel Roe <>
Date: Tue, 14 Aug 2012 09:04:10 -0600


The RMS command by default performs a best-fit rotation on coordinates
(unless 'nofit' is specified) in addition to centering, while the
center command performs centering only. So in the second command the
coordinates are being rotated to minimize the RMSD to the coordinates
in the first frame, so you are in essence performing 'atomicfluct' on
different coordinates than in the first case, which is why you get
different answers.

Hope this helped,


On Tue, Aug 14, 2012 at 8:45 AM, Eliac Brown <> wrote:
> Dear All
> I was wondering what is the difference between the RMS fitting and the usual fitting command of (center :X-XX mass origin).
> The Center command beside it reallocates the atoms into the origin of the box, it does also perform RMS fit (see page 112 AMBERTOOLS 1.4 manual).
> So, why I got different answers when I calculated the RMSF per residue with the following jobs:
> Job I
> trajin 1ns.mdcrd
> atomicfluct out RMSF :1-100 byres
> Job II
> trajin 1ns.mdcrd
> rms first :1-100
> atomicfluct out RMSF :1-100 byres
> Note that the 1ns.mdcrd is already centers in both cases using
> center :1-100 mass origin
> image origin center
> Any kind of explanation would be highly appreciated
> Cheers
> _______________________________________________
> AMBER mailing list

Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
(801) 587-9652
(801) 585-9119 (Fax)
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Received on Tue Aug 14 2012 - 08:30:04 PDT
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