[gmx-users] I have a question about 'How h_bond module in Groamcs compute Hydrogen bond correlation function '
ghdyd158 at unist.ac.kr
Fri Mar 11 11:04:12 CET 2016
Hello, I'm an user of Gromacs who want to calculate hydrogen bond life time in various system. I know that we can use h_bond module with -ac option to get hydrogen bond lifetime between two groups but I want to make sure that how those correlation function comes out.
I analyzed trajectroy of each hydrogen pairs and I could make existence function ( h(t) ) for each tagged h_bond pair and I computed correlation function but It shows different pattern from I got from -ac option.
Can anybody tell me how hydrogen bond correlation function is computed in Gromacs from trajectroy?
I read paper of Luzar ,Chandler and Van der Spoel more than 10 times and I know all those definition. What I want to know is how practically we can compute it.
Thank you for reading my message!!!
Sincerely, Ho Yong
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