Molecular Dynamics wrote:
Dear Gromacs Users,
I’m interested in n-alkanes and evaluating thermophysical and
structural properties of n- alkanes and binary mixtures of n-alkanes.
I want to use Gromacs and the force fields in Gromacs for my n-alkanes
simulations. And I want to ask some questions to you. First, I’m
planning to generate a packmol pdb file that includes 100 molecules for
pure and binary mixtures. Can I directly use this pdb file with pdb2gmx
? Can I use the partial charges generated with Gaussian for n-alkanes
molecules ? If so, what is the procedure of this ? How can I load the
partial charges into Gromacs ? And Finally, I want to use both all atom
and United atom force fields. Could you suggest me some force fields
that can be used for n-alkanes md simulations ?
Perhaps you have the cart somewhat ahead of the horse. I would start by
reading the literature to see what sorts of simulations other people
have done. You'll see what force fields and software they used, and can
start learning what tools you should consider using. Presupposing
particular pieces of software and/or forcefields is a good way to come
unstuck.
Mark
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