[gmx-users] Hydrogen Bond Residence Time

[Erik Marklund]

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/