[gmx-users] pairwise h-bonds

bernhard morpheus.sommer2008 at gmail.com
Fri Aug 21 12:45:04 CEST 2015

Dear Gromacs users,

I was wondering about the best way of obtaining pairwise h-bonds of certain

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?


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