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
--
Thanks a lot for your attention,
Best Regards,
Nahid
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Received on Sat Apr 11 2015 - 00:30:02 PDT
