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

[maria goranovic]

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
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