[gmx-users] g_rotacf again

Tsjerk Wassenaar tsjerkw at gmail.com
Wed Sep 27 11:47:31 CEST 2006

Hi Rama,

You would be able to do it by taking one of two approaches:

1. Write the centers of masses and from this generate a multipdb file
(or gro file) containing three atoms spanning two vectors
perpendicular to the vector between these centers of masses. This
trajectory can be used for g_rotacf (although you may need a proper
run input file to go with it), according to the description given by
g_rotacf -h.

2. Hack gmx_rotacf.c to calculate the rcf of the vector betwee centers
of masses rather than between the cross product of two vectors between
three atoms given.

I think the latter option is easiest (if you can program a bit).

Hope it helps,


On 9/27/06, Rama Gullapalli <quantrum75 at yahoo.com> wrote:
> Hello everybody.
> I have question regarding g_rotacf
> If I wanted to compute the rotational correlation function of a linear
> vector which is between the "centers of masses" of two groups of atoms in an
> individual molecule (Instead of two atoms), how do I go about it?
> Can I use g_rotacf to do it ?
> Thanks in advance
> Rama
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Tsjerk A. Wassenaar, Ph.D.
Groningen Biomolecular Sciences and Biotechnology Institute (GBB)
Dept. of Biophysical Chemistry
University of Groningen
Nijenborgh 4
9747AG Groningen, The Netherlands
+31 50 363 4336

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