[gmx-users] water mediated Hbond

Justin Lemkul jalemkul at vt.edu
Mon May 13 15:58:22 CEST 2019

On 5/13/19 8:48 AM, Bratin Kumar Das wrote:
> Hi,
>       You can make a ndx file containing the residue of interest and the
> SOL. In gmx h-bond command use the index file. It will give you water
> mediated hbond

That's not what a water-mediated hydrogen bond is. That's when a water 
molecule simultaneously participates in hydrogen bonds with two other 
species. GROMACS does not have the ability to do such calculations 
easily. It would require one calculation of H-bonds between species A 
and water, saving those waters into index groups per frame, and then 
computing the H-bonds of those waters with species B in a separate 
calculation. Only then do you get the number of water-mediated (not 
direct) hydrogen bonds.


> On Tue 7 May, 2019, 12:40 PM , <spss4 at iacs.res.in> wrote:
>> Dear all
>> I want to determine the water mediated hydrogen between DNA bases and
>> small molecule. What extra flag should I use in gmx hbond command? Is
>> there any other option to capture the water mediated Hbonds? Please
>> suggest something.
>> Sunipa Sarkar
>> --
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Justin A. Lemkul, Ph.D.
Assistant Professor
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