[gmx-users] Hbonds and PBC

[Justin A. Lemkul]

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

-- 
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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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