[gmx-users] pairwise h-bonds

Erik Marklund erik.marklund at chem.ox.ac.uk
Sat Aug 22 22:03:26 CEST 2015

Dear Morpheus,

Try the -hbn and -hbm options. The latter generates a similar matrix and the former is essentially a dictionary to that matrix.

Kind regards,

> On 21 Aug 2015, at 12:45, bernhard <morpheus.sommer2008 at gmail.com> wrote:
> Dear Gromacs users,
> I was wondering about the best way of obtaining pairwise h-bonds of certain
> residues.
> I got about 100 residues of interest and 1000 simulation frames. I would
> like to get the h-bonds at each timeframe between each pair of residues.
> i.e. a matrix with 100x100x1000. At the moment I have  created an index
> group for each residue and run the pairwise h-bond calculations in two
> nested loops via a perl script. The problem is that this takes long and
> also creates 10 000 000 files on the harddisk which I then need to parse
> with another skript.
> Is there an easier way? I have also tried to use the -m option with protein
> and protein as input groups but this also those not give the pairwise
> h-bonds but rather the cumulative ones per residue against all 100 residues.
> Can anyone give me a hint?
> Cheers,
> Morpheus
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