I'm trying to get the electrostatic potential for a simple DMPC lipid bilayer using the following command:
gmx potential -f traj.trr -s topol.tpr -n index.ndx -o potential.xvg -d z -correct
Though the electrostatic potential profile that I obtain is similar to those reported, the absolute values do not match. The plot obtained shows the same profile but with positive V values. However, the electron density profiles (of all components in the system - P, CH2, water etc.) match perfectly with the reported values.
Can you please tell me where I could be going wrong?
Thanks in advance.