[gmx-users] pairwise h-bonds

[Erik Marklund]

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
> -- 
> Gromacs Users mailing list
> 
> * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
> 
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> 
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org.