[gmx-users] pairwise h-bonds

bernhard morpheus.sommer2008 at gmail.com
Mon Aug 24 10:46:14 CEST 2015

Sorry I had a typo in my previous email: I have used the -hbm and -hbn
option (not the -m as it does not exist).

The problem is however that this option gives me the h-bonds for each
residues of group 1 to _any_ residue of group 2 and not the pairwise
h-bonds between all members of group 1 and group 2. i.e. it gives a
100x1000 matrix instead of a 100x100x1000 matrix.

I guess I am not the first person enountering this problem so there must be
a quite simple solution got get all pairwise h-bonds but I can't figure it
out ...


> Erik Marklund erik.marklund at chem.ox.ac.uk
> Sat Aug 22 22:03:26 CEST 2015
>     Previous message: [gmx-users] pairwise h-bonds
> 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,
> Erik
> On 21 Aug 2015, at 12:45, bernhard <morpheus.sommer2008 at gmail.com>
> Dear Gromacs users,
> I was wondering about the best way of obtaining pairwise h-bonds of
> 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
> 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
> Can anyone give me a hint?
> Cheers,
> Morpheus

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