GROMACS version: 2018.8
GROMACS modification: No
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Hello,
we are trying to reproduce the Lifetime of water (Nature 379:55, 1996) using the theory of Luzar and Chandler, but the Forward rate k and Backward rate k ’ calculated by the program are not the same order of magnitude, k’ is very small, so we want to know what happend in the calculation of H-bond?
GROMACS command : gmx hbond –f .xtc –s .tpr –ac
It is the gromacs out info, and the k` is so strange:
Hydrogen bond thermodynamics at T = 298.15 K
Fitting parameters chi^2 = 4.23175
Q = 0
Type Rate (1/ps) Time (ps) DG (kJ/mol) Chi^2
Forward 0.172 5.813 8.891 4.23175
Backward 0.000 58132.344 31.723
One-way 0.330 3.033 7.278
Integral 0.165 6.049 8.990
Relaxation 0.232 4.309 8.149
We believe that the problem occurred in the fourth column of the program output file (S2 legend “Cc\scontact,hb\v{}\z{}(t)”), which was extremely jitter, resulting in inaccurate data from k and K 'fitting. So what do we want to know about this column? And how to get stable data.
Here is a picture of " Cc\scontact,hb\v{}\z{}(t)" which I think is the n(t) mentioned in the luzar article.
(dt=0.5fs, trj time = 250ps, output traj for each step)
Thank in advance