GROMACS version: 2020
GROMACS modification: No
Hello,
I am using gmx hbond with the -ac and -life options to determine the average hydrogen bond lifetimes in my system. When I run the command, I get the following output:
Type Rate (1/ps) Time (ps) DG (kJ/mol) Chi^2
Forward 0.169 5.908 8.931 1.48156
Backward 0.000 6843.424 26.420
One-way 0.332 3.009 7.259
Integral 0.603 1.657 5.780
Relaxation 5.025 0.199 0.526
HB lifetime = 1.03 ps
From my understanding of the GROMACS documentation and the provided literature, the lifetime can be calculated as the inverse of the forward rate constant. However there is a discrepancy between the value obtained in this way (5.908 ps) and the one provided in the last line of the output (HB lifetime = 1.03 ps).
I have also tried, as indicated in the documentation, doing a multiexponent fit to the autocorrelation function output and integrating the obtained function to get the average hydrogen bond lifetime. The value I get is also very different from both values obtained from the output.
Accordingly, I would really appreciate it if someone could help answer the following questions:
-
What is the reason for the discrepancy between the two values (5.908 vs 1.03 ps) obtained from the GROMACS output?
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What are the one-way and relaxation values obtained in the output?
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Is the lifetime value obtained using the multiexponent fit + integration approach more meaningful than those obtained automatically from the output?
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What considerations need to be taken into account when using the gmx hbond utility to analyze hydrogen bonding between two protein chains?
Thanks in advance!