[gmx-users] I have a question about 'How h_bond module in Groamcs compute Hydrogen bond correlation function '

백호용 (자연과학부) 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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