anyone ? :) On Fri, Jul 22, 2011 at 1:19 PM, maria goranovic <mariagorano...@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 Copenhagen
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