Thank you for the reply.
By the way, is there any way to look at only small part of a molecule for rotational motion?
Regards
Vijay Manickam Achari
(Phd Student c/o Prof Rauzah Hashim)
Chemistry Department,
University of Malaya,
Malaysia
vjramana.gmail.com
________________________________
From: David A Case <case.biomaps.rutgers.edu>
To: Vijay Manickam Achari <vjrajamany.yahoo.com>; AMBER Mailing List <amber.ambermd.org>
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.
...dac
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Received on Wed Oct 02 2013 - 19:30:04 PDT
