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 (www.bioelectrophysics.org). You can find a subset of these in Dr. Zach Levine's website (http://www.zachlevine.com/downloads.html).
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.