[gmx-users] autocorrelation output g_hbond
erikm at xray.bmc.uu.se
Mon Jun 17 16:06:53 CEST 2013
…or the hydrogen-bond kinetics of your system may not fit the Luzar-Chandler model for whatever reason.
On 17 Jun 2013, at 13:22, Erik Marklund <erikm at xray.bmc.uu.se> wrote:
> 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
>> Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
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