[gmx-users] gmx analyze Luzar analysis

Erik Marklund erik.marklund at kemi.uu.se
Tue Aug 29 14:01:42 CEST 2017

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 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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