shahab shariati skrev 2010-11-24 16.24:
Dear gromacs users
I used g_hbond -f .trr -s .tpr -n .ndx -ac -life.
Can anyone clarify last 2 columns in hblife.xvg and last 4 columns
hbac.xvg
files by details. Also, I want to know what is difference between p(t)
in hblife.xvg and c(t) in
hbac.xvg file? which of them is more suitable for HB lifetime?
any help will highly appreciated
For hblife, I don't know. in hbac.xvg the first column is the
autocorrelation function (acf) with a (somewhat dubious) correction to
compensate for a finite system (the acf sohuld approac zero for large
distances, but for a periodic finite system the tail is proprotional to
1/N, N being the number of particles). The second one is the 'raw' acf.
Third column is the cross correlation between the hb-existence functions
and corresponding contact-existence function (contacts fulfil the
distace criterium but not the angular criterium). The fourth column is
the derivative of the first column.
The problem with -life, as far as I know, is that it models the hbond
breaking/formation as a simple one step process, which may not be a good
description. See the Luzar and Chandler papers for the theory behind the
constants reported by g_hbond -ac. Therefore I'd use -ac to determine
the rate for hb breaking.
Cheers,
--
-----------------------------------------------
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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