[gmx-users] Fwd: charges,resonance and electrostatics
omermar at gmail.com
Wed Sep 24 14:56:19 CEST 2008
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.
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