[gmx-users] Calculating hydrogen bonds between specific residues

Agnivo Gosai agnivogromacs14 at gmail.com
Fri Jan 30 03:00:11 CET 2015

Dear Users

I want to calculate the number of hydrogen bonds occurring between two
residues A and B in my biomolecule complex from a production MD run over
the course of the simulation time.

I am thinking of the following strategy :-

1. Create an index file containing the residue numbers from the .gro file
of my production run.
2. Feed the index file to " g_hbond" , select the two residues of interest
and run the command.

My questions are :

a) While calculating H-bond should I use should I use -nonitacc tag for
physiological pH ? I am not sure as I do not know the pH value of my
system. I neutralized the system with Na and Cl ions such that the final
conc is 0.1 M.

b) In general is my procedure a correct way of using "g_hbond" ?

Kindly help.

Thanks & Regards
Agnivo Gosai
Grad Student, Iowa State University.

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