Executable: D:\software\gmx2022.6_GPU\bin\gmx.exe
Data prefix: D:\software\gmx2022.6_GPU
Working dir: C:\Users\Administrator\Desktop\waterbox
Command line:
gmx hbond -f prod.xtc -s prod.tpr -num -life -nhbdist -nomerge
Back Off! I just backed up nhbdist.xvg to ./#nhbdist.xvg.1#
Reading file prod.tpr, VERSION 2022.6 (single precision)
Specify 2 groups to analyze:
Group 0 ( System) has 2652 elements
Group 1 ( Water) has 2652 elements
Group 2 ( SOL) has 2652 elements
Select a group: 0
Selected 0: 'System'
Select a group: 0
Selected 0: 'System'
Calculating hydrogen bonds in System (2652 atoms)
Found 884 donors and 884 acceptors
Making hbmap structure...done.
Reading frame 0 time 0.000
Will do grid-search on 7x7x7 grid, rcut=0.34999999
Frame loop parallelized with OpenMP using 16 threads.
Last frame 500 time 1000.000
Found 362602 different hydrogen bonds in trajectory
Found 435446 different atom-pairs within hydrogen bonding distance
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Average number of hbonds per timeframe 1532.200 out of 390728 possible
++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
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 --- -------- --------
HB lifetime = 2.19 ps
Note that the lifetime obtained in this manner is close to useless
Use the -ac option instead and check the Forward lifetime
++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
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 --- -------- --------
GROMACS reminds you: "I Smell Smoke From a Gun Named Extinction" (Pixies)
Doing autocorrelation according to the theory of Luzar and Chandler.
ACF 30018/30018
Normalization for c(t) = 0.00268054 for gh(t) = 2.65351e-05
Hydrogen bond thermodynamics at T = 298.15 K
Fitting parameters chi^2 = 0.000122375
Q = 0
--------------------------------------------------
Type Rate (1/ps) Time (ps) DG (kJ/mol) Chi^2
Forward 1.559 0.641 3.427 0.000122375
Backward -0.002 -466.651 -666.000
One-way 3.095 0.323 1.727
Integral 0.185 5.404 8.710
Relaxation 0.153 6.519 9.175
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HB lifetime = 5.34 ps
Note that the lifetime obtained in this manner is close to useless
Use the -ac option instead and check the Forward lifetime