Dear jit mukherjee,
You might find it usefull to check Gromacs site.
We did some work with Gromacs and nanotubes:
M. Kaukonen, A. Gulans, P. Havu, E. Kauppinen, J. Comput. Chem. 2012,
33, 652–658. DOI: 10.1002/jcc.22884
But things may have changed and periodic nanotubes could be doable
also with Amber?
I don't know the current situation, checked it last time about 2 years ago.
Terveisin, Markus
On 25 May 2012 09:18, FyD <fyd.q4md-forcefieldtools.org> wrote:
> Dear jit mukherjee,
>
>> I want to simmulate carbon nanotube system using AMBER. It cab be done
>> with antechamber. Is this possible to generate the topology file by
>> not using the antechamber,i.e., by using the ff99SB force field?
>
> I would check how QM geometry optimization goes for carbon nanotube
> and fullerene systems in sqm, Gaussian etc... Read literature about
> theory levels used in QM. You can test different QM programs at R.E.D.
> Server...
>
> Then, I would check how chemical equivalencing is handled by
> Antechamber. From what I heard chemical equivalencing should now
> handled by Antechamber. However, I am not sure this new approach works
> for this type of molecular systems; I mean for molecular systems of
> big size + with multiple cycles. We tested our algo. in Ante_R.E.D.
> 2.0 and for sure chemical equivalencing is not correctly handled. So
> we developed a totally new/fast algo. that seems to handle such
> complex cases. It is not yet available yet. I hope we will release
> examples in R.E.DD.B. soon to demonstrate this new feature...
>
> regards, Francois
>
>
>
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> http://lists.ambermd.org/mailman/listinfo/amber
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--Markus.Kaukonen.iki.fi
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Received on Fri May 25 2012 - 00:00:05 PDT
