[gmx-users] n-alkanes simulations in Gromacs

Mark Abraham Mark.Abraham at anu.edu.au
Sat Feb 28 12:10:27 CET 2009

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 


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