Omer Markovitch wrote:
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.
There is no non-bonded interaction between these two oxygens, unless you are
using an Urey-Bradley potential for the angle, like in the CHARMM force field.
Most (if not all) of the standard force fields in Gromacs treat the interaction
of these oxygens within an angle definition, which is a bonded term.
-Justin
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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--
========================================
Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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