[gmx-users] Unanswered Query regarding hydrogen bond lifetime and energy
apramita.chand at gmail.com
Tue Dec 20 20:02:30 CET 2016
> 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?
More information about the gromacs.org_gmx-users