[gmx-users] Re: g_bundle -na option for calculating angle between helices

maria goranovic mariagoranovic at gmail.com
Mon Jul 25 11:17:54 CEST 2011

anyone ? :)

On Fri, Jul 22, 2011 at 1:19 PM, maria goranovic
<mariagoranovic at gmail.com>wrote:

> Hi
> I am trying to calculate angle between helices using g_bundle and:
> http://lists.gromacs.org/pipermail/gmx-users/2007-October/030415.html
> <http://lists.gromacs.org/pipermail/gmx-users/2007-October/030415.html>I
> am unable to understand how the -na option works. "the program reads 2 index
> groups and divides them into na parts". I will use -na 2 for 2 axes. But
> what should the index groups be? with -na 1 I would use the CA atoms on the
> top and bottom of the helix as the 2 index groups. For 2 helices, should the
> first index group be the CA atoms at the beginning of the 2 helices? Or
> should the first index group contain top and bottom CA atoms on the same
> helix, and the second index group should contain the same for the second
> helix?
> Thank you for clarifying
> --
> Maria G.
> Technical University of Denmark
> Copenhagen

Maria G.
Technical University of Denmark
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