[gmx-users] How Gromacs h_bond module compute hydrogen correlation function ?
erik.marklund at chem.ox.ac.uk
Mon Mar 14 11:22:26 CET 2016
Gromacs uses FFTs to calculate C(t), exploiting that convolutions (such as an autocorrelation) turns into simple muliplications in Fourier space. If you are interested in the details, have a look at gmx_hbond.c. In the function do_hbac(), look for the last call to low_do_autocorr() and the code around it. It should be under “case AC_LUZAR:”. There may be other calls to low_do_autocorr(), depending on your version, but they concern other kinetic models and alternative bond definitions that aren’t fully supported.
> On 12 Mar 2016, at 07:13, 백호용 (자연과학부) <ghdyd158 at unist.ac.kr> wrote:
> 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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