[gmx-users] How Gromacs h_bond module compute hydrogen correlation function ?

백호용 (자연과학부) ghdyd158 at unist.ac.kr
Sat Mar 12 08:28:17 CET 2016

Dear gromacs users and developers, I have a question about the methodology that gromacs h_bond module compute H_bond correlation function, C(t) from trajectory.

I want to compute hydrogen bond life time between a carbonyl oxygen of single Etoac and water. For example, I made a system which contain a single Etoac molecules and about 2000 water molecules. then I used h_bond module to get hbmap.xpm and hbond.ndx and I analyzed those two so that I can get existence function of each carbonyl oxygen - water pair. In detail, during 500 ps simulation, 23 water molecules formed hydrogen bond with carbonyl oxygen of Etoac at least one time. So, I computed 23 existence functions, each having 500 ps length. Then I use those 23 set of existence function to compute h_bond correlation function.

I'll upload Matlab code (corr_031116.m )with which I computed correlation function and please tell me what the problem is..

So, What I want to know is that How Gromacs practically compute Correlation function, in detail..

Thank you for reading my email and Thank you for your reply in advance..

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