[AMBER] a question for hydrocarbons simulation using amber FF

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From: Nahid Khiabani <nahidkhiabani.gmail.com>
Date: Thu, 9 Apr 2015 13:33:43 -0700

Dear all

Hope you are fine.

I am using amber FF according to this paper
(http://www.ncbi.nlm.nih.gov/pubmed/14531054) also
(http://www.ncbi.nlm.nih.gov/pubmed/15116359) to simulate a system
including some alkane molecules such as hexane. I am using LAMMPS package
to do the simulation.

To define an alkane molecule such as hexane I have defined its bonds,
angles and dihedrales according to the 2 versions of amber forcefield. For
non-bonded interactions I also have defined LJ and Columbic pair
potentials.

I am wondering if I also need to consider
special_bonds(http://lammps.sandia.gov/doc/special_bonds.html) for this
type of molecules?

Thanks a lot for your attention,
Best Regards,
Nahid
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Received on Thu Apr 09 2015 - 14:00:02 PDT