[gmx-users] selecting two groups for average structure

Justin A. Lemkul jalemkul at vt.edu
Wed Sep 9 02:31:39 CEST 2009

David Crosby wrote:
> Hello, I'm sure there's a simple solution to this problem, so please bear
> with me...  I'm attempting to generate an average structure from a
> trajectory and I'd like to have it pool two groups into the final structure.
> I work with a magnesium-coordinating integrase protein, so my groups are 1:
> protein, and 12: MG2+.  Trying to average each then combine the two files
> won't work as the ions are re-centered in coordinate space after the
> averaging is done.

Merge the two groups using make_ndx, and pass this index file to whatever 
utility programs you are using.


> Thanks!
> Dave Crosby
> University of California, Irvine
> Dept of Pathology and Laboratory Medicine
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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