[gmx-users] autocorrelation function and residence time

Tasneem Kausar tasneemkausar12 at gmail.com
Wed Sep 20 06:12:35 CEST 2017

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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