[gmx-users] fraction of native contacts calculation
bipinelmat at gmail.com
Thu Nov 1 20:03:44 CET 2012
Thanks a lot Oliver for the useful information.
On Fri, Nov 2, 2012 at 12:26 AM, Oliver Beckstein <obeckste at asu.edu> wrote:
> >>> 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
> (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
> Office: PSF 348
> Phone: +1 (480) 727-9765
> FAX: +1 (480) 965-4669
> Department of Physics:
> Center for Biological Physics:
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