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.
________________________________________________________________________
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
[email protected] [email protected] http://folding.bmc.uu.se
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