[gmx-users] Questions about hydrogen bond lifetime

Jian Dai djpittdj at gmail.com
Sun Dec 6 05:54:04 CET 2009

Hi, dear all (especially for David):
When reading the paper "Thermodynamics of hydrogen bonding in hydrophilic
and hydrophobic media" and its supplementary material and the code
"gmx_hbond.c" for the analysis of hydrogen bond, I got questions:
1. When calculating the autocorrelation function of the interrupted lifetime
using -ac option, is the error of the calculation given by "Chi^2" in the
2. As can be seen from the supplementary material of the paper, the forward
and backward rate k and k' are dependent on the temperature, but from the
code, I can not identify the link between "temp" and "k" since "temp" is
only used in "calc_dg()", which means "temp" and "k" are not related. Am I
Thank you.
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