AMBER Archive (2002)

Subject: Re: removing rotational motion

From: Jianxin Guo (guojx_at_yahoo.com)
Date: Fri Feb 22 2002 - 16:32:48 CST

Considering the aim of the MD run is to obtain the
relative movement of the atoms in your system, it is
nice to remove translationa and rotational motions of
your system. If amber can not control the rotation,
simply find the rotaional matrix for your system which
can be defined by the mass of center, moment of
initial etc, and do transformation for all atoms
(coordinate and velocity). implementing it after the
code that amber removes translation. the main problem
may be in how to deal with solvent near the boundary
of the cell. If you cell is big enough and the rotaion
is small for each transformation, then it is ok,
otherwise, there will be some difficulty. Or instead,
a simpler solution is to make fit of your trajectory.
correct me please if I am wrong.
Jianxin

Date: Tue, 19 Feb 2002 13:30:00 +0100 (CET)
From: Raik Grunberg <raik_at_pasteur.fr>
Subject: Re: removing rotational motion
Message-ID:
<Pine.OSF.4.21.0202191326400.277935-100000_at_electre.pasteur.fr>

translation can be removed with nscm=<step interval>,
however, removal of
rotation seems indeed not to be available.

Raik

On Tue, 19 Feb 2002, John Finke wrote:

|
|I noticed that, in AMBER 6, the option for removing
rotational and
|translational motion is no longer available.
|
|Am I mistaken? If not, is there an easy way to
implement the removal of
|these motions.
|
|Sincerely,
|
|John Finke
|jfinke_at_ucsd.edu

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