[gmx-users] g_hbond -ac -life

[Erik Marklund]

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
erikm at xray.bmc.uu.se    http://folding.bmc.uu.se/