[gmx-users] Hydrogen bond occupancy for the dimer of Acetic Acid

Ran Friedman r.friedman at bioc.uzh.ch
Thu Nov 12 15:12:31 CET 2009

Hi Rasmus,

A simple solution would be to run g_hbond twice, with two separate
groups for acetate 1 as donor and acetate 2 as acceptor or vice versa,
check the existence an hydrogen bond with g_hbond -num and write a
script to check when the two hydrogen bonds co-exist.

Hope that helps,

Rasmus "Termo" Lundsgaard wrote:
> Hi All.
> I'm trying to calculate the Hydrogen bond occupancy when there is two
> hydrogen bonds between same two acetic acid molecules at the same time.
> With g_hbond I can get the hbond.ndx giving me "all ocuring hydrogen
> bonds" group and the hbmap.xpm gives me the matrix of when these
> hydrogen bonds exist for each timeframe...
> How can I calculate the occupancy of when two hydrogen bonds exist
> between the same two molecules??
> Best regards
> Rasmus

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