Re: [AMBER] rotational diffusion error

From: Daniel Roe <>
Date: Fri, 4 Oct 2013 08:11:19 -0600


On Wed, Oct 2, 2013 at 8:06 PM, Vijay Manickam Achari
<> wrote:
> By the way, is there any way to look at only small part of a molecule for rotational motion?

Well, the 'rotdif' action was developed with the aim of looking at the
rotational diffusion of an entire molecule in solution. You could I
suppose specify only part of a molecule to use when calculating the
rotation matrices, but I'm not sure how you would interpret the
results. The region needs to be at least 3 atoms large, otherwise
RMS-fitting doesn't make sense.


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) 585-6208 (Fax)
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Received on Fri Oct 04 2013 - 07:30:10 PDT
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