Re: [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 :

> 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.markl...@kemi.uu.se
>
> On 29 Aug 2017, at 13:52, Valerio Ferrario  mailto:valerio.ferra...@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 0.006156.395   17.174
> Integral  -0.076- 13.220-666.000
> Relaxation  1.0380.963 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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Re: [gmx-users] gmx analyze Luzar analysis

[Erik Marklund]

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.markl...@kemi.uu.se

On 29 Aug 2017, at 13:52, Valerio Ferrario 
mailto:valerio.ferra...@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 0.006156.395   17.174
Integral  -0.076- 13.220-666.000
Relaxation  1.0380.963 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?
--
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

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[gmx-users] gmx analyze Luzar analysis

[Valerio Ferrario]

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 0.006156.395   17.174
Integral  -0.076- 13.220-666.000
Relaxation  1.0380.963 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?
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

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