[gmx-users] autocorrelation function and residence time

Erik Marklund erik.marklund at kemi.uu.se
Thu Sep 21 11:24:08 CEST 2017

Dear Tasneem,

Quite often ACF calculations involve subtraction of the average signal, and this normally renders some negative values in the ACF. It’s been a bit too long since I dealt with the gmx hbond code, but I suspect that is what is going on here. I suggest reading the references that gmx hbond mentions, where the four quantities in the output are defined.

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 21 Sep 2017, at 11:12, Tasneem Kausar <tasneemkausar12 at gmail.com<mailto:tasneemkausar12 at gmail.com>> wrote:

Still waiting for suggestions.

On Wed, Sep 20, 2017 at 9:42 AM, Tasneem Kausar <tasneemkausar12 at gmail.com<mailto:tasneemkausar12 at gmail.com>>

Dear all

I want to calculate residence time of interface water molecules at protein
interface. I am using Gromacs-4.6.4.
I am using using following command
g_hbond -s protein.tpr -f protein.xtc -b 2000 -n proein.ndx -ac
protein_ac.xvg -contact
In the index file there are protein interface residues and  8 water
molecule that are present at the protein interface. I have selected protein
interface and 8 water for calculation. In the output of autocorrelation
there are four y axis columns. I came through reply of Erik. He mentioned
the effect of periodic boundary condition on the output. In my case first y
axis has several negative values. I want to do an exponential fit with
function y=exp(-(x/t)^n) to obtain value of t and b. Can we skip the
negative values of the output file? If yes what is the reason to do that.
If I am wrong please suggest me to do the right way to obtain residence

Thanks in Advance

Tasneem Kausar

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