[gmx-users] autocorrelation output g_hbond
learnmd
joinforfun8909 at gmail.com
Sat Jun 15 00:38:40 CEST 2013
Hi,
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.
Thanks
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