[gmx-users] Re: Using lennard jones and buckingham terms simultaneously

Vitaly V. Chaban vvchaban at gmail.com
Tue Mar 23 16:04:38 CET 2010

And how will protein and carbonate interact with one another according
to your model?

Look towards tabulated potentials - with them you can perform any miracles. :)

Dr. Vitaly Chaban

> I would like to use gromacs-4 to do a simulation of a small protein in water
> and in the presence of calcium carbonate.  The potential I have for the
> calcium carbonate uses Buckingham terms for the interaction between the
> calcium and carbonate ions, while the protein obviously interacts through
> Lennard Jones terms.  It is my understanding from the manual that it is not
> possible to mix these two interaction types and so it is not possible to do
> this simulation.  Also when I attempted to mix lennard jones and buckingham
> terms in a topol.top file grompp complained.
> Is there anyway around this problem?
> Many thanks
> Gareth

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