[gmx-users] HB lifetime in g_hbond

[David van der Spoel]

Patricia Soto Becerra wrote:
> Hi,
> I have a question regarding the calculation of hydrogen bond lifetimes 
> in g_hbond:
> 
> Line 1094 of gmx_hbond.c v 1.16.2.11 2006/04/02 (which is equivalent to 
> line 1121 of gmx_hbond.c v 1.28 2006/08/30) reads:
> 
> t  = hb->time[i] - hb->time[0] - 0.5*dt;
> 
> leading to the time series 1, 3, 5,.. that does not correspond to my 
> sampling frequency of 2ps. This affects the calculation of x1 in the 
> immediate next line. My question is: Why is t defined in this way?
> 
The program computes an histogram and centers the points in between time 
points. Note that this flag gives you useless lifetimes, see J. Phys. 
Chem. B 110 pp. 4393-4398 (2006). You want to use the lifetime that 
comes from the -ac option (look at line with Forward)

-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se
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