From: Luca Muccioli (luca_at_ms.fci.unibo.it)
Date: Wed Oct 28 2009 - 15:31:38 CDT
if all the atoms are chemically equivalent (in other words, they have exactly
the same electronegativity) and the molecule is neutral, the partial charges
should be zero. Think at the N2 molecule as example, or at a united atom model
for benzene, or to an infinite graphene sheet.
If you want partial, fluctuating charges on such molecules you have to use
polarizable force fields.
for fullerene derivatives of course the situation is different, due to the
On Wed, 28 Oct 2009, Austin B. Yongye wrote:
> Date: Wed, 28 Oct 2009 09:41:49 -0700 (PDT)
> From: Austin B. Yongye <ybausty_at_yahoo.com>
> To: Luca Muccioli <luca_at_ms.fci.unibo.it>
> Cc: NAMD list <namd-l_at_ks.uiuc.edu>
> Subject: Re: namd-l: Fullerene topology
> Thanks Luca.
> Will take a look at the file.
> Are there any reasons why those charges are set to zero, other than approximations? I am in the process of generating partial charges (using antechamber) to reproduce the QM-derived molecular electrostatic potential of some derivatized fullerenes. I'll see whether the charges are sufficiently low to be set to zero. I'll also impose charge symmetry, and might perform the same exercise with the underivatized fullerene.
> Thanks for the response, references and the topology file.
> --- On Wed, 10/28/09, Luca Muccioli <luca_at_ms.fci.unibo.it> wrote:
>> From: Luca Muccioli <luca_at_ms.fci.unibo.it>
>> Subject: Re: namd-l: Fullerene topology
>> To: "Austin B. Yongye" <ybausty_at_yahoo.com>
>> Cc: "NAMD list" <namd-l_at_ks.uiuc.edu>
>> Date: Wednesday, October 28, 2009, 8:55 AM
>> 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 I'am doing some (still unpublished) studies C60, I use the
>> carbon parameters of the GAFF/AMBER force field
>> and they work reasonably well (the
>> crystal cell constants are very similar to experimental
>> 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.
>> 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.
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