In gromacs ,on using -life option we get the following answer
Type Rate (1/ps) Time (ps) DG (kJ/mol) Chi^2
Forward 0.149 6.692 9.313 0.00998919
Backward 0.589 1.699 5.894
One-way 0.126 7.910 9.730
Integral 0.055 18.056 11.789
Relaxation 0.091 11.019 10.557
HB lifetime = 0.85 ps
Note that the lifetime obtained in this manner is close to useless
Use the -ac option instead and check the Forward lifetime
So what should be the actual hydrogen bond lifetime? The uninterrupted hydrogen bond lifetime should be 0.85ps or 6.69(forward lifetime)? What about structural reorganisation time? Is it same as relaxation time defined here?
you need to calculate what is popularly known as continuous H-bond time correlation function S(t), which is not provided in gromacs as far as I know.
You can consult the following paper.
http://journals.aps.org/prl/abstract/10.1103/PhysRevLett.89.115505
Thank you for your answer. Then what do these values in gromacs refer to?
For instance, forward lifetime=6.692 ps? or the value written as HB lifetime=0.85ps?
What are these values exactly?
I would use the g_hbond -ac autocorrelation analysis option using the method developoed by Luzar and Chandler.
- Badges
- Science topic