[gmx-users] n-alkanes simulations in Gromacs

Molecular Dynamics amberquestion at yahoo.com
Sat Feb 28 11:58:36 CET 2009

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 ?
Thanks in advance
Kind regards

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