[gmx-users] Hbonds and PBC

Justin A. Lemkul jalemkul at vt.edu
Tue Jun 12 16:41:51 CEST 2012

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 A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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