Could someone tell me how to calculate the electrostatic potential across the z axis of a lipid bilayer ? Also, I would like to calculate the potential from the lipid headgroup to a specific point of the z axis.
You may have to read about the Computational Electrophysiology (CompEL) protocol:
C. Kutzner, H. Grubmüller, B.L. de Groot, and U. Zachariae, “Computational electrophysiology: The molecular dynamics of ion channel permeation and selectivity in atomistic detail,” Biophys. J., 101 809–817 (2011).
Justin Lemkul Could you please tell me how to use gmx potential from a specific atom group along the z axis ? because until now, I only have achieved to get the potential across the whole simulation box.