Hi all,
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.
Thank you in advance
Hi Laura,
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).
Calculation of electrostatic potential is pretty straight forward in VMD. You can even do it using their GUI:
https://www.ks.uiuc.edu/Research/vmd/plugins/pmepot/
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.
Thank you in advance.
That's what the program does. But you can compute the potential for any group of atoms via an index group, like any GROMACS program.
Justin Lemkul So if I calculate the potential for a selected molecular part of, let's say, a membrane embedded protein, then I get the contribution of selected molecular part to the overall electrostatic potential of the system at the given z coordinate of the box?
Thank you in advance.
Attila Borics I have no experience doing that kind of calculation but you should investigate the source code closely to see if the program can reliably do that kind of calculation. It's designed specifically for bilayers; I do not know if its calculations work for parts of proteins.
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