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.
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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
[email protected] http://folding.bmc.uu.se/
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