[gmx-users] hydrogen bond

Erik Marklund erikm at xray.bmc.uu.se
Tue Jan 12 14:16:36 CET 2010

leila karami skrev:
> Hi
> I want to obtain following parameters about water molecule and 
> hydrogen bonds in pr-dna simulation:
> 1) residence time of number of water mediated hydrogen bonds
> 2) life time of number of water mediated hydrogen bonds
> 3) number of water mediated hydrogen bonds
> 4) number of direct hydrogen bonds
> Do g_hbond command is suitable for all of case mentioned above?
> Any help will highly appreciated!
Yes and no. Only 4 in your list above is available directly. IF you're 
willing to do some sort of programming in pretty much any preferred 
language, you can extract 1-3 from the existence matrix of all hydrogen 
bonds and its complementary index file (options -hbm and -hbn). 
Lifetimes probably requires a bit more work, as the autocorrelation of 
the existence function is needed, but there are plenty of tools for 
that, e.g. xmgraxe or perhaps g_analyse.

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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