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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