[gmx-users] g_hbond -ac -life
erikm at xray.bmc.uu.se
Wed Nov 24 16:37:30 CET 2010
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
> 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.
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/
More information about the gromacs.org_gmx-users