On 6/12/12 10:39 AM, Steven Neumann wrote:
Dear Gmx Users,
Do I have to get rid of pbc from my trajectory in order to calculate number of
hydrogen bonds using g_hbond? I mean: Does pbc has any influence on the number
of hydrogen bonds?
Nearly all Gromacs analysis tools deal with periodicity. g_hbond only needs to
measure simple distances and angles, which should be unaffected by PBC. Try it
and see.
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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