[gmx-users] autocorrelation output g_hbond

learnmd joinforfun8909 at gmail.com
Sat Jun 15 00:38:40 CEST 2013


I have run a 5 ns simulation with a small protein in water [SPCE]. I am
interested in the rate of breakage (sense of how quickly / slowly hbonds are
broken and formed) of hbonds between protein and solvent. I ran g_hbond -ac
for the trajectory and received the following output:

Normalization for c(t) = 0.0204961 for gh(t) = 4.55478e-07
Hydrogen bond thermodynamics at T = 298.15 K
Fitting parameters chi^2 =  0.0335188
Q =          0
Type      Rate (1/ps) Time (ps)  DG (kJ/mol)  Chi^2
Forward         0.022     46.303      14.035   0.0335188
Backward       -0.080    -12.447    -666.000
One-way         0.068     14.603      11.175
Integral        0.020     48.944      14.173
Relaxation      0.052     19.211      11.854

My question is that the 46 ps that is shown for "forward" can be interpreted
in the sense that I have described above?  Or am I missing the point,
completely. I am grateful for any pointers. 


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