[gmx-users] autocorrelation function and residence time

Tasneem Kausar tasneemkausar12 at gmail.com
Thu Sep 21 11:12:06 CEST 2017

Still waiting for suggestions.

On Wed, Sep 20, 2017 at 9:42 AM, Tasneem Kausar <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
> time.
> Thanks in Advance
> Tasneem Kausar

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