Hello, There is a point, I want to clear out for myself: Say we focus on the aspartate residue. It has a formal charge of -1. This charge on either oxygen of the carboxyl is -0.8 (oxygens OD1 & OD2), according to one of the force fields employed in GROMACS.
What is the right way to calculate electrostatics here: 1) "As is", and letting the two oxygens repel one another. 2) Ignore this specific pair when calculating? How does GROMACS operates? I think that (1) is the common practice, but I want to be sure. Thank you, Omer Markovitch. (this email was sent to gmx-dev. by mistake) Koby Levy research group, Weizmann Institute of Science. http://www.weizmann.ac.il/sb/faculty_pages/Levy/
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