[gmx-users] gmx hbond

Erik Marklund erik.marklund at kemi.uu.se
Tue Feb 6 10:30:20 CET 2018

Hi Negar,

Correct, the -dist option doesn’t do what you want it to. I cannot come up with a recipe for how to do this, but I suspect multiple rounds of gmx select and gmx hbond might do the trick.

Kind regards,
Erik Marklund, PhD, Marie Skłodowska Curie INCA Fellow
Department of Chemistry – BMC, Uppsala University
+46 (0)18 471 4539
erik.marklund at kemi.uu.se<mailto:erik.marklund at kemi.uu.se>

On 5 Feb 2018, at 15:49, negar habibzadeh <negarhze at gmail.com<mailto:negarhze at gmail.com>> wrote:


I want to calculate *number of hydrogen bond* by *distance from center of
i use gmx hbonds -dist but it doesn't give me the proper result.is<http://result.is> it true?
which options should i implement to get the best result?

best regads
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