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 calculate in that way.
I made a list of all hydrogen bonds for every frame, but I modified data to have a list of hydrogen bonds, as not atom number, but molecule number like
Then I compare a list of hydrogen bonds from every frame always to the first frame and I print to output these hydrogen bonds which are present in both frames (present and first).
Then I calculate water bridges. So for example in the first frame, I have 480 water bridges, so I calculate that: 480/480 = 1, then in the third frame I have 240 water bridges, so I have 240/480 = 0,5, then in the 1000th frame 120, so 120/480 = 0,25.
And now there is a time for a question. If I havefor example hydrogen bonds like
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
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