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

Rasmus "Termo" Lundsgaard termopeten at gmail.com
Thu Nov 12 15:04:03 CET 2009

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

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