[gmx-users] hydrogen bonds

Justin A. Lemkul jalemkul at vt.edu
Fri Jul 30 17:58:10 CEST 2010

Vasilis Georgilas wrote:
> Hello everyone,
> in the NPT simulation I run I have 2 layers of water and palmitic acid 
> in between.
> How i should make my index file to see the different kinds of hydrogen 
> bonds?
> ps
> there will be water - water , O= ..... O= between PLM, O= ...... OH 
> between PLM and water and OH .... OH between water and PLM hydrogen bonds

Then you need groups for each of these moieties (water should be a default 
group), and you'll have to do several runs of g_hbond to collect all of the 
pairs you want to analyze.


> thanks in advance
> Regards,
> Vasilis


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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