[gmx-users] autocorrelation output g_hbond

[Erik Marklund]

Hi,

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.

Erik

On 15 Jun 2013, at 00:38, learnmd <joinforfun8909 at gmail.com> wrote:

> 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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