[gmx-users] Hydrogen Bond Residence Time

Erik Marklund erikm at xray.bmc.uu.se
Wed May 5 15:54:27 CEST 2010

Anirban Ghosh skrev:
> Hi ALL,
> How can I obtain the residence time of each hydrogen bond during a 
> simulation? I think the -hbn and -hbm options of g_hbond has to be 
> used, but how? Is there any script to extract that data? And what is 
> the difference between the residence time and the life time of a 
> hydrogen bond? Any suggestion is welcome.
> Thanks a lot in advance.
> Regards,
> Anirban
g_hbond calculates the lifetime of all analyzed hydrogen bonds from the 
ACF according to Luzar and Chandler's model. You can run g_hbond several 
times to get the lifetime of all hydrogen bonds. It will be time 
consuming though. The information is indeed in the hbm matrix from a 
single run of g_hbond with all hbonds analyzed, but there's no script 
that I know of that extracts it for you. You need to build individual 
ACFs for every hbond, and they will probably all be very noisy, giving 
very large error bars.

Erik Marklund, PhD student
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://folding.bmc.uu.se/

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