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)
Yes, I had indeed noticed that the value reported by this flag was far
from my own calculations so I wanted to make sure I was understanding what
g_hbond was doing. Thanks. (of course, I already read your paper in JPC
B.)
Patricia
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