[gmx-users] LJ question

David van der Spoel spoel at xray.bmc.uu.se
Thu Aug 28 19:34:30 CEST 2008

Anthony Cruz wrote:
> Dear Users:
> I am planing to do some simulations of a protein in acetonitrile using the 
> model of P.J. Gee (Mol. Phys. (2006) 104, 477-483). The use of this model 
> will introduce new atom types and new LJ parameters for those atoms. When I 
> define those atoms in the acetonitrile topology I need to define the mixing 
> of LJ for all the atoms or gromacs will do it?

Make sure that you have a force field that allows mixing. OPLS will do 
the trick.
> Cheers,
> Anthony
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David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se

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