[gmx-users] gmx analyze Luzar analysis

[Valerio Ferrario]

Thank you!

But still I do not understand what those values represents since there
isn´t a legend in the gmx analyze output. I understood that those 3 values
should be the average hbond lifetime, and the 2 constant k and k´. Am I
correct ?

The fitting is bad since I used long simulation time analysis... Reducing
the time I obtain the same relaxation values With better integrals:

Hydrogen bond thermodynamics at T = 300 K
One-way         0.030     33.376      13.321
Integral           0.085     11.729      10.713
Relaxation      1.038      0.963       4.478

Valerio


2017-08-29 14:01 GMT+02:00 Erik Marklund <erik.marklund at kemi.uu.se>:

> Dear Valerio,
>
> Have a glance at the paper by Luzar and Chandler.
>
> Btw: your data doesn’t fit with the kinetic model very well, hence the
> -666 for the integral.
>
> Kind regards,
> Erik
> ______________________________________________
> Erik Marklund, PhD, Marie Skłodowska Curie INCA Fellow
> Department of Chemistry – BMC, Uppsala University
> +46 (0)18 471 4539
> erik.marklund at kemi.uu.se<mailto:erik.marklund at kemi.uu.se>
>
> On 29 Aug 2017, at 13:52, Valerio Ferrario <valerio.ferrario at gmail.com<
> mailto:valerio.ferrario at gmail.com>> wrote:
>
> Dear all,
>
> I am trying to obtain parameters for h-bonds. I used the tool gmx hbonds
> with -ac option but resulted in segmentation fault. Therefore from the
> normal gmx hbond output I used gmx analyze to obtain the autocorrelation
> function. Therefore, using again gmx analyze with -luzar options and the
> autorrelated xvg as input I want to calculate the hbonds parameters. I have
> an output like this:
>
> Hydrogen bond thermodynamics at T = 300 K
> One-way         0.006    156.395       17.174
> Integral          -0.076    - 13.220    -666.000
> Relaxation      1.038        0.963         4.478
>
> So my question is: what are the different values? I do not understand what
> those values indicate since no "legend" is provide. I guess that 2 of the 3
> values for relaxation might be k and k´ (rate constant for breaking and
> reforming hbonds), but I am not sure... Can anyone help me in interpreting
> those numbers?
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