[gmx-users] Checking the existence of a hydrogen bond network

Erik Marklund erik.marklund at chem.ox.ac.uk
Thu Apr 16 17:28:18 CEST 2015

Dear Max,

You will need to use the -hbm and -hbn options to generate the existance function for all hydrogen bonds over time. Parsing those files requires a bit of work, but is certainly doable.

Kind regards,

> On 16 Apr 2015, at 12:59, Ebert Maximilian <m.ebert at umontreal.ca> wrote:
> Dear list,
> I am trying to find a possibility with standard gromacs tools to verify in every frame if two residues are interconnected through a hbonds with a water molecule. My initial idea was to evaluate the hbonds of both residues per frame and write a small bash script looking for frames in which both residues hbonded with the same water molecule. However, I could’t find an option in gmx hbond to write out the hbonds per frame except for the number of hbonds per frame and a file with all partners. Before starting to have to loop over every frame individually and start gmx hbond as often as the number of frames I wanted to know if there is an easier approach to what I want to do.
> Basically I want to know how long this bridge existed over the course of the simulation.
> Thank you very much,
> Max
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