[gmx-developers] charges,resonance and electrostatics

Erik Marklund erikm at xray.bmc.uu.se
Wed Sep 24 18:20:29 CEST 2008

Omer Markovitch skrev:
> 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.
> Koby Levy research group,
> Weizmann Institute of Science.
> http://www.weizmann.ac.il/sb/faculty_pages/Levy/
As far as I know this depends on the force field. Most force fields 
ignores non-bonded interactions connected by fewer than three bonds, as 
is the case with the oxygens in aspartate. Non-bonded interactions 
between atoms separated by three bonds are often scaled down by a "fudge 

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Erik Marklund, PhD student
Laboratory of Molecular Biophysics,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,    75124 Uppsala, Sweden
phone:    +46 18 471 4537        fax: +46 18 511 755
erikm at xray.bmc.uu.se    http://xray.bmc.uu.se/molbiophys

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