Actually, I have asked on the LAMMPS mailing list. They said that I should
ask this question from the force-field developers. This is why I have
emailed to the Amber maling list.
Thanks,
Best,
Nahid
On Sun, Apr 12, 2015 at 3:50 AM, <hannes.loeffler.stfc.ac.uk> wrote:
> I'm not sure why you keep reposting your question but your best bet is
> probably to ask this on the LAMMPS mailing list.
> ________________________________________
> From: Nahid Khiabani [nahidkhiabani.gmail.com]
> Sent: 12 April 2015 11:33
> To: amber.ambermd.org
> Subject: [AMBER] a question for hydrocarbons simulation using amber FF
>
> 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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>
--
Thanks a lot for your attention,
Best Regards,
Nahid
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Received on Sun Apr 12 2015 - 04:00:03 PDT
