On Sat, Apr 11, 2015, Nahid Khiabani wrote:
>
> 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?
It is unlikely that anyone of this list knows the answer to your questions,
which is specific to LAMMPS. As I understand the reference, you do need
this term, which in amber jargon is equivalent to setting scee and scnb.
...dac
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Received on Sun Apr 12 2015 - 06:30:02 PDT
