[gmx-users] Questions about hydrogen bond lifetime

David van der Spoel spoel at xray.bmc.uu.se
Sun Dec 6 09:46:12 CET 2009

Jian Dai wrote:
> 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 output?
Don't know.

> 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 right?

You have to do simulations at different Temperature.'

Do also check this paper which we are busy implementing in the program:
Reversible geminate recombination of hydrogen-bonded water  molecule pair
Omer Markovitcha and Noam Agmonb THE JOURNAL OF CHEMICAL PHYSICS 129, 
084505 2008

> Thank you.
> Jian

David van der Spoel, PhD, Professor of Biology
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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