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

Apramita Chand apramita.chand at gmail.com
Fri Dec 9 12:19:45 CET 2016

Dear All,
 Is there any way to calculate hydrogen bond energy in GROMACS ? Or at
least any information which could be applied from GROMACS to calculate the

Also,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
Select a group: 15
Selected 15: 'Water'
Select a group: 15
Selected 15: 'Water'
Calculating hydrogen bonds in Water (2892 atoms)
Found 964 donors and 964 acceptors
Making hbmap structure...done.
trn version: GMX_trn_file (single precision)
Reading frame       0 time    0.000
Will do grid-seach on 8x8x8 grid, rcut=0.35
Last frame      15000 time 15000.000
Found 453844 different hydrogen bonds in trajectory
Found 460098 different atom-pairs within hydrogen bonding distance
Merging hbonds with Acceptor and Donor swapped
- Reduced number of hbonds from 453844 to 453844
- Reduced number of distances from 460098 to 460098

Back Off! I just backed up hbnum.xvg to ./#hbnum.xvg.2#
Average number of hbonds per timeframe 1498.831 out of 464648 possible

D. van der Spoel, P. J. van Maaren, P. Larsson and N. Timneanu
Thermodynamics of hydrogen bonding in hydrophilic and hydrophobic media
J. Phys. Chem. B 110 (2006) pp. 4393-4398
-------- -------- --- Thank You --- -------- --------

Doing autocorrelation according to the theory of Luzar and Chandler.
ACF 453844/453844
Normalization for c(t) = 0.000667222 for gh(t) = 4.44762e-08

Back Off! I just backed up hbac.xvg to ./#hbac.xvg.2#
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?

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