[gmx-users] pairwise h-bonds

Erik Marklund erik.marklund at chem.ox.ac.uk
Wed Aug 26 12:35:45 CEST 2015


Note however that each line is a specific donor-acceptor pair. All the information you need is in that matrix and the corresponding index file.

Kind regards,

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

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

> On 24 Aug 2015, at 09:46, bernhard <morpheus.sommer2008 at gmail.com> wrote:
> 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 ...
> Best,
> Morpheus
>> 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>
> 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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