Re: [AMBER] rotational diffusion error

From: Vijay Manickam Achari <>
Date: Thu, 3 Oct 2013 03:06:38 +0100 (BST)

Thank you for the reply.

By the way, is there any way to look at only small part of a molecule for rotational motion?


Vijay Manickam Achari
(Phd Student c/o Prof Rauzah Hashim)
Chemistry Department,
University of Malaya,

 From: David A Case <>
To: Vijay Manickam Achari <>; AMBER Mailing List <>
Sent: Wednesday, 2 October 2013, 19:34
Subject: Re: [AMBER] rotational diffusion error

On Wed, Oct 02, 2013, Vijay Manickam Achari wrote:
> rotdif nvecs 1000 ref [avg] :DDM.C15,C16 ncorr 90 ti 0.0 tf 0.80 dt
> 0.002 deffout deffs.dat itmax 500 tol 0.000001 d0 0.03 order 2 outfile
> rotdif.out

Do you really only have two atoms in your mask (":DDM.C15,C16")?  I think this
might be a degenerate case where the rotation matrices are not well-defined.

Also, have you visualized the trajectory?  Is the system undergoing rotational
tumbling?  Be sure you can do a "standard" calculation (e.g. where the mask
covers the entire backbone, or the entire backbone that is in secondary
structure), and can understand the results.  As I pointed out in an earlier
email, the rotdif command is not suited to analyze rotational behavior of just
part of system.

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Received on Wed Oct 02 2013 - 19:30:04 PDT
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