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

Ran Friedman r.friedman at bioc.uzh.ch
Thu Nov 12 16:22:09 CET 2009

Hi Rasmus,

>From your previous email I understood that you have only two molecules
(you didn't write that you're using 500 and nothing on the rest of the
system). Apparently, this is not the case. I don't think you can get
what you want from g_hbond without modifying the source code.  If you
don't mind 500 runs you can use g_dist -dist, where group 1 is a single
hydrogen bond donor oxygen and group two all potential acceptors, find
the molecules which satisfy your criterion and then run g_hbond on them
if you want to be sure that you have a hydrogen bond that satisfy angle
criteria as well. Tedious, but can work with some scripting and patience.


Rasmus "Termo" Lundsgaard wrote:
> Hi Ran.
> If I understand you right, then you suggest to have one molecule as
> acceptor, and the rest (499) as donors, and then look in the hbnum.xvg
> to see how often there is two hydrogen bonds...
> 1. is that I have to do this check for every molecule.
> 2. there is no guaranty that the two hydrogen bonds are to the same
> other molecule - it could very well be as a part of a chain...
> 3. If possible I would like to do measurement of distance between
> molecules when they are bonded as a dimer...
> Best regards
> Rasmus
> Ran Friedman wrote:
>> 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,
>> Ran.
>> 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

Ran Friedman
Postdoctoral Fellow
Computational Structural Biology Group (A. Caflisch)
Department of Biochemistry
University of Zurich
Winterthurerstrasse 190
CH-8057 Zurich, Switzerland
Tel. +41-44-6355559
Email: r.friedman at bioc.unizh.ch
Skype: ran.friedman

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