[gmx-developers] Implementation of H-bond analysis

Erik Marklund erikm at xray.bmc.uu.se
Thu Feb 12 13:25:38 CET 2009


I second that. What you intend to do sounds much easier to implement in 


Ran Friedman skrev:
> Hi,
> The easiest option seems to modify gmx_hbond so that you get the D-H-A
> index file as frequently as you want it, unless you really need to use
> this as an input during your md simulations.
> Ran.
>> Dear developers,
>> At this first step of my project I want to change gromacs in that way to
>> do a h_bond-analysis every nth step.
>> I wish to get an Donor-hydrogen-acceptor index file from my current
>> structure of my simulated protein after for example every 10th step.
>> After this change in mdrun.h, md.c or stat.c I would like to have 10
>> D-H-A index files after 100 md steps.
>> I need this kind of output for further implementations after this
>> frequent h-bond-analyses.
>> The h-bond tool produces with input -hbn the same D-H-A index list, but
>> externally.
>> Greetings,
>> Emanuel
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Erik Marklund, PhD student
Laboratory of Molecular Biophysics,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,    75124 Uppsala, Sweden
phone:    +46 18 471 4537        fax: +46 18 511 755
erikm at xray.bmc.uu.se    http://xray.bmc.uu.se/molbiophys

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