[gmx-users] Regarding error in hydrogen bond lifetime

Apramita Chand apramita.chand at gmail.com
Fri Dec 9 07:17:45 CET 2016

Dear All,
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

*Select a group: 15Selected 15: 'Water'Select a group: 15Selected 15:
'Water'Calculating hydrogen bonds in Water (2892 atoms)Found 964 donors and
964 acceptorsMaking hbmap structure...done.trn version: GMX_trn_file
(single precision)Reading frame       0 time    0.000   Will do grid-seach
on 8x8x8 grid, rcut=0.35Last frame      15000 time 15000.000   Found 453844
different hydrogen bonds in trajectoryFound 460098 different atom-pairs
within hydrogen bonding distanceMerging hbonds with Acceptor and Donor
swapped964/964- Reduced number of hbonds from 453844 to 453844- Reduced
number of distances from 460098 to 460098Back Off! I just backed up
hbnum.xvg to ./#hbnum.xvg.2#Average number of hbonds per timeframe 1498.831
++++D. van der Spoel, P. J. van Maaren, P. Larsson and N.
TimneanuThermodynamics of hydrogen bonding in hydrophilic and hydrophobic
mediaJ. Phys. Chem. B 110 (2006) pp. 4393-4398-------- -------- --- Thank
You --- -------- --------Doing autocorrelation according to the theory of
Luzar and Chandler.ACF 453844/453844Normalization for c(t) = 0.000667222
for gh(t) = 4.44762e-08Back Off! I just backed up hbac.xvg to
./#hbac.xvg.2#Hydrogen bond thermodynamics at T = 298.15 KFitting
parameters chi^2 = 0.00780548Q =
0--------------------------------------------------Type      Rate (1/ps)
Time (ps)  DG (kJ/mol)  Chi^2Forward         0.201      4.968       8.502
0.00780548Backward        0.530      1.885       6.100One-way
0.208      4.817       8.425Integral        0.069     14.445
11.148Relaxation      0.119      8.377       9.797Back Off! I just backed
up h_w.vg.xvg to ./#h_w.vg.xvg.1#HB lifetime = 3.50 psNote that the
lifetime obtained in this manner is close to uselessUse the -ac option
instead and check the Forward lifetime*.

So , is the forward 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?


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