[gmx-users] gmx potential for membrane electrostatic potential

Sahithya S Iyer sah2714 at gmail.com
Thu Jun 14 18:12:19 CEST 2018

Hi gmx users,

I am 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 -sl
1000 --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.
The electron density profiles (of all componenets in the system - P, CH2,
water etc) match perfectly with the reported values.

Can you please tell me where I could be going wrong.


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