[gmx-users] Unanswered Query regarding hydrogen bond lifetime and energy

[Apramita Chand]

> Dear All,

> Let me repeat my earlier query.
> I'm trying to calculate the hydrogen bond lifetime in my system
(water-ethanol) using command g_hbond -f traj.trr -s md.tpr  -n index.ndx
-ac -life hblife.xvg. It is peculiar to note that when I select index
groups as OW and HW (for water), it finds 0 hydrogen bonds! But when I
select water and water from the index file, it shows the hydrogen bond
lifetime to be
> Average number of hbonds per timeframe 1498.831 out of 464648 possible
> Doing autocorrelation according to the theory of Luzar and Chandler.
> ACF 453844/453844
> Normalization for c(t) = 0.000667222 for gh(t) = 4.44762e
> Hydrogen bond thermodynamics at T = 298.15 K
> Fitting parameters chi^2 = 0.00780548
> Q =          0
> --------------------------------------------------
> Type      Rate (1/ps) Time (ps)  DG (kJ/mol)  Chi^2
> Forward         0.201      4.968       8.502  0.00780548
> Backward        0.530      1.885       6.100
> One-way         0.208      4.817       8.425
> Integral        0.069     14.445      11.148
> Relaxation      0.119      8.377       9.797
>
> Back Off! I just backed up h_w.vg.xvg to ./#h_w.vg.xvg.1#
> HB lifetime = 3.50 ps
> Note that the lifetime obtained in this manner is close to useless
> Use the -ac option instead and check the Forward lifetime.

So , is lifetime 4.968 or 3.50 ps? Also, should I divide the value by 2
since there are two hydrogens in water ?
>
> Next, in water-ethanol hydrogen bonds, if I give the groups as Oethanol
and water, and OW , ethanol   , I get different lifetimes but get fatal
error as no 'hydrogen bonds' if I try specifying the exact two sites like
OW-HEthanol or Oethanol-HW1.
> Why is this happening?

Regards,
Apramita