[gmx-users] Hydrogen bond existence map

Erik Marklund erik.marklund at chem.ox.ac.uk
Thu Jun 19 12:24:07 CEST 2014

Hi Nidhi,

Only with post processing of named files I'm afraid.

Kind regards,

On 19 Jun 2014, at 10:48, Nidhi Katyal <nidhikatyal1989 at gmail.com> wrote:

> Hi all
> I would like to create hydrogen bond existence map for interaction of each
> residue with my ligand. I am aware that -hbm and -hbn option of g_hbond
> along with index file would serve the purpose. But the resulting output
> file is giving existence map for each atom of the residue. Instead, I want
> one map for residue as a whole. Example if any residue of protein is
> forming hydrogen bond with my ligand for certain time through bond A but
> for the remaining time it forms through bond B, then I want the map to show
> presence of hydrogen bond through one single line during the entire course
> of simulation. Is it possible with gromacs?
> Thanks in advance
> Nidhi
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