Esin B. Sözer

Research Assistant Professor

Frank Reidy Research Center for Bioelectrics

Laboratory of multiscale bioelectrical interactions

I developed these MATLAB scripts to analyze electropore characteristics from a trajectory file output of GROMACS. The scripts can be used for centering of an electropore in the simulation box, measuring the pore radius with water or with P/N atoms of lipids (in our case a POPC bilayer), transport through a pore, and the PN dipole angle of lipids in any POPC bilayer. I suggest starting with RunPoreCenterRadiusConductance.m, which is the main script that has the calls for rest of the functions.

I got help from Federica Castellani for design, test and debugging of the functions and most of this work is inspired by prior studies led by Tom Vernier ( You can find a subset of these in Dr. Zach Levine's website (

Feel free to contact me if you would like to use these scripts and need help to adapt them for your simulations. I don't guarantee they are error-free. If you use them please contact me for the right citation.