GROMACS version: 2018.4 GROMACS modification: No I have a question. I want to know one thing. How is computing autocorrelation function, because I am not sure about something.
I try to calculate the autocorrelation function by myself. This is what I get when I calculate the autocorrelation function for water bridges. (I add the picture in attachments)
I calculate in that way.
And now there is a time for a question. If I have for example hydrogen bonds like MGD100 SOL1000 and I have this hydrogen bond in the first frame and in the second frame, but then in the third, fourth, fifth, sixth, seventh, eighth, ninth frame I don’t have this hydrogen bond, but then in the tenth frame this hydrogen bond appears again, so should I count this hydrogen bonds or not (it was not existing for an 8 ps). On the one hand, it is both in the first frame and tenth frame, but on the other hand, it was not existing for 8 ps (1 frame in my case is 1 ps).
I found gmx hbond file, but I can’t find my answer https://raw.githubusercontent.com/gromacs/gromacs/master/src/gromacs/gmxana/gmx_hbond.cpp
Or maybe you know, who was programming gmx hbond program, because when I write in my terminal gmx hbond I have a big list of persons and I don’t know, which person I should contact
:-) GROMACS - gmx hbond, 2018.4 (-: GROMACS is written by: Emile Apol Rossen Apostolov Paul Bauer Herman J.C. Berendsen Par Bjelkmar Aldert van Buuren Rudi van Drunen Anton Feenstra
Gerrit Groenhof Aleksei Iupinov Christoph Junghans Anca Hamuraru Vincent Hindriksen Dimitrios Karkoulis Peter Kasson Jiri Kraus Carsten Kutzner Per Larsson Justin A. Lemkul Viveca Lindahl Magnus Lundborg Pieter Meulenhoff Erik Marklund Teemu Murtola Szilard Pall Sander Pronk Roland Schulz Alexey Shvetsov Michael Shirts Alfons Sijbers Peter Tieleman Teemu Virolainen Christian Wennberg Maarten Wolf and the project leaders: Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel
Hi,
I think first you should read the papers that were the basis for gmx hbond (especially the first one):
D. van der Spoel, P. J. van Maaren, P. Larsson, N. Tmneanu, J. Phys. Chem. B 2006, 110, 4393–4398.
A. Luzar, J. Chem. Phys. 2000, 113, 10663 –10675.
A. Luzar, D. Chandler, Nature 1996, 379, 55–57.
And why do you ever want to calculate it for water molecules?
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