[gmx-users] Zinc parameters

Mark Abraham mark.abraham at anu.edu.au
Thu Aug 3 14:47:01 CEST 2006

> Hello.
> Can somebody help me. I want to create ansemble of zinc atoms.
> Zinc atoms are not charged. What parameters of Lennard Jones potential
> need to take?

Depends whether you want to model real physics or not :-)

> Can I take the Lennard Jones parameters for zinc ions
> and apply them to ansemble of zinc atoms, they are not bonded.

No. Forcefields are sets of parameters designed to interact as a whole as
a physical model. If you have only zinc atoms, then you need to find a
source of physical information about how uncharged zinc atoms behave, pick
a mathematical functional form to model that, and produce parameters that
model your physical information. Have a read of some of the papers
referenced in the GROMACS manual that describe the development of the
biomolecular forcefields for some ideas here.


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