[gmx-users] calculation of total no of hydrogen bond present in the system

[Erik Marklund]

Dear Rahman,

The donors are not the hydrogens, but the oxygens to which they are bonded.

Kind regards,
Erik


Erik Marklund, PhD
Postdoctoral Research Fellow
Fulford JRF, Somerville College

Department of Chemistry
Physical & Theoretical Chemistry Laboratory
University of Oxford
South Parks Road
Oxford
OX1 3QZ

> On 23 Jun 2015, at 11:08, MOHD HOMAIDUR RAHMAN <rahmanhpu at gmail.com> wrote:
> 
> Dear All Gromacs users
> 
> I am try to calculate total no of hydrogen bond present in a system. For
> that I am using gromacs 5.0.2 (gmx hbond ). The problem is that I am unable
> to specify donor and acceptor during input. I am using Amber coordinate and
> topology file that is converted to gromacs topology and coordinate through
> acpype.py. Now how to specify no of donor and acceptor for water molecules.
> 
> Total 350 water molecules is there in my system . So there should be two H
> bond donor and two H bond acceptor, but during calculation it is showing
> 350 donor and 350 acceptor.
> 
> Thanks
> ​Rahman​
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