[gmx-users] pairwise h-bonds
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.
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 ...
>> 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,
>> 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
>> 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?
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