[gmx-users] How Gromacs H_bond module compute hydrogen bonding correlation function practically and in detail?

백호용 (자연과학부) ghdyd158 at unist.ac.kr
Tue Mar 15 18:12:20 CET 2016

Dear all gromacs users and developers

I make my own code based on definition introduced on paper of Luzar, Chandler and Van der Spoel and compute correlation function so that It can have initial value of 1 and approach to 0 as time goes on. I plot computed correlation function together with correlation function that h_bond module compute(2.jpg, blue - my correlation, green - gromacs_no_corrected and red-gromacs_corrected ) and I found that they have almost same pattern but has totally different y value except for t = 0. So, It seems I'm close to the result but I'm still not understanding some important thing...

What I want to know is actually that how practically gromacs h_bond module computes hydrogen bond correlation from trajectory. I read related papers so many times and I know the procedure that we define existence function and compute the correlation function of them and also I know the definition. But, still I'm had difficulty in getting exactly same correlation function as what h_bond modules compute.

So, If Anybody know that in very detail and practically how gromacs h_bond module compute the hydrogen bond correlation function, Please let me know...

I'm struggling with this problems more than 3 months and I'm exhausted.. Again,

What I want is not general but detailed and practical procedure that gromacs h_bond module actually take.

Thank you for reading my question and I'm look forward to your reply !!

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