[gmx-users] autocorrelation output g_hbond

[Erik Marklund]

…or the hydrogen-bond kinetics of your system may not fit the Luzar-Chandler model for whatever reason.

Erik

On 17 Jun 2013, at 13:22, Erik Marklund <erikm at xray.bmc.uu.se> wrote:

> 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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