[gmx-users] autocorrelation output g_hbond
erikm at xray.bmc.uu.se
Mon Jun 17 13:22:25 CEST 2013
Yes, the forward and backward rate constants are for hydrogen-bond breaking and reforming. You seem to have too poor statistics to draw conclusions about the backward rate, however. You probably need to simulate longer.
On 15 Jun 2013, at 00:38, learnmd <joinforfun8909 at gmail.com> wrote:
> 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.
> View this message in context: http://gromacs.5086.x6.nabble.com/autocorrelation-output-g-hbond-tp5009171.html
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