[gmx-users] fraction of native contacts calculation

Oliver Beckstein obeckste at asu.edu
Thu Nov 1 19:56:12 CET 2012

>>> Is there any way to calculate fraction of native contacts during the
>>> simulation in gromacs. I searched the archives but didn't found any
>>> significant clue.
>> At present, there is no way to do this.  Likely one could modify the g_mindist code to do this - it would be a very nice feature.
> If one could get the -sel option of g_hbond to work again then you would get such information with -contact.

In the meantime you might be able to use MDAnalysis http://mdanalysis.googlecode.com/ and the native contact analysis in MDAnalysis.analysis.contacts, see http://packages.python.org/MDAnalysis/documentation_pages/analysis/contacts.html

(If you have questions about MDAnalysis then please ask them on that project's discussion group http://groups.google.com/group/mdnalysis-discussion — people there are more than happy to help.)

Best wishes,

Oliver Beckstein * oliver.beckstein at asu.edu

Arizona State University
Department of Physics
Tempe, AZ 85287-1504
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