Re: Fullerene topology

From: Luca Muccioli (luca_at_ms.fci.unibo.it)
Date: Wed Oct 28 2009 - 10:55:11 CDT

dear Austin,

  as far as I can see all atoms on C60 are chemically equivalent, that means that
if you do not want to break the symmetry you should have only one atom type and
all the charges are zero.

I'am doing some (still unpublished) studies C60, I use the aromatic
carbon parameters of the GAFF/AMBER force field
(http://ambermd.org/antechamber/gaff.html) and they work reasonably well (the
crystal cell constants are very similar to experimental ones).

About the simulation references, I know there are a lot of papers of Michael L.
Klein published in the early ninenties, and some more recent ones:
Abramo et al PRE 69, 031112 (2004)
Liu et al J. Phys. Chem. C 2008, 112, 4687-4695
Cantrell, Clancy SURFACE SCIENCE Volume: 602 Issue: 22 Pages: 3499-3505 2008

I attach my topology of C60 (the format is not for NAMD but it is easy to
adapt) and the corresponding pdb file.

cheers

Luca

-------------------------------------------

Luca Muccioli, Ph. D.
Dipartimento di Chimica Fisica e Inorganica, INSTM
Universita` di Bologna
Via Risorgimento 4
40136 Bologna (Italia)

E-mail: luca_at_fci.unibo.it
Phone: +39-051-6446992
Fax: +39-051-2093690
Web: http://www2.fci.unibo.it/~luca/

On Mon, 26 Oct 2009, Austin B. Yongye wrote:

> Date: Mon, 26 Oct 2009 11:40:17 -0700 (PDT)
> From: Austin B. Yongye <ybausty_at_yahoo.com>
> To: NAMD list <namd-l_at_ks.uiuc.edu>
> Subject: namd-l: Fullerene topology
>
> Hi everyone,
> Has anyone performed simulations of fullerenes (C60 in particular) with NAMD using CHARMm parameters? I saw a question in the mailing list back in 2007, but no response.
>
> If yes, how were the atom types and charges set up for the 5,6 bridges, given that these atoms are part of the aromatic six-membered and non-aromatic five-membered rings? Also, there is less electron density the 5,6 bridges compared to the 6,6 bridges.
>
> I came across Dr. Coluci's paper:
> Rotational dynamics and polymerization of C60 in C60-cubane crystals: A molecular dynamics study Coluci et al. J. Chem. Phys. 129, 064506 (2008)
>
> but was wondering whether others have done NAMD fullerene simulations as well.
>
> Thanks,
> Austin-
>
>
>
>

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