[gmx-users] LJ question
David van der Spoel
spoel at xray.bmc.uu.se
Thu Aug 28 22:16:57 CEST 2008
Anthony Cruz wrote:
> Thank you for your rapidly responce David. If I use thr Gromos96 (ff43a1) it
> will do it? How I check if the force field allows mixing?
GROMOS does not use mixing rules in the same way as other force fields.
This means it is more cumbersome, though not impossible. I'm not sure
whether there are parameters for the N in aceotonitrile either. Please
read e.g. the Oostenbrink paper.
> On Thursday 28 August 2008 01:34:30 pm David van der Spoel wrote:
>> 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.
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David van der Spoel, Ph.D., Professor of Biology
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se
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