Re: simulation of fullerenes

From: Adam Fraser (adam.n.fraser_at_gmail.com)
Date: Wed Dec 05 2007 - 12:31:45 CST

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I just read this reply to a message sent in 2004 (below). If there are
specific forcefield parameters developed to handle fullerenes, could someone
please let me know? Previously, I was considering using the CA atom type in
par_all22_prot...

CA CA 305.000 1.3750 ! ALLOW ARO
! benzene, JES 8/25/89

..now I'm doubtful.

-Adam

Re: psf file for zeolite-water system

*From:* Fangqiang Zhu
(*fzhu_at_ks.uiuc.edu*<fzhu_at_ks.uiuc.edu?Subject=Re:%20%20psf%20file%20for%20zeolite-water%20system>
)
*Date:* Mon Feb 23 2004 - 14:16:26 CST

Hi,

Technically this is possible. There's no force field parameter developed
specifically for CNTs or fullerenes so far. In recent publications of MD
simulations of CNTs, people usually use the parameters for sp2 carbons
(e.g., carbons on benzene rings) from traditional force fields, to describe
carbon atoms of CNTs (the charge was set to 0). No one knows how
accurately such parameters could model CNTs in real world. But if
you trust them, you can go ahead and do a MD simulation...

Zhu

$B:,>k(J $B6Q(J wrote:

*> Dear NAMD users; *
*> This is really good question. I am also a new NAMD user. *
*> I would like to calculate the interaction between *
*> carbon nanotubes, fullerenes inside CNT and amine outside CNT. *
*> All these are nonbonded interactions between them. *
*> Are these calculations possible? *
*> Thanks in advance. *
*> Hitoshi *
*> > *
*> > I am a new NAMD user. I am trying to do MD simulations for water *
*> > molecules confined in Zeolite pores. Zeolite is basicly a network of
SiO2 *
*> > molecules. I created a pdb file for my water zeolite system
successfuly, *
*> > well that was the easy part. I know Si atom is not supported by Charmm
*
*> > topology file. So I cant create a psf file. Zeolite structure has only
*
*> > nonbonded interactions with water molecules. How should I modify the *
*> > topology file? How can I use psfgen tool to create a psf file for this
*
*> > system? or should I forget NAMD for this system? *
*> > *
*> > Any advice would be appreciated. *
*> > *
*> > -- *
*> > Ozgur YAZAYDIN *
*> > Research Assistant *
*> > Department of Chemical Engineering *
*> > Worcester Polytechnic Institute *
*> > 100 Institute Road, Worcester, MA 01609-2280 *
*> > *
*> > *
*> *
*> ------------------------------------------------------------- *
*> Hitoshi Nejo $B!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!:,>k!!6Q(J *
*> National Institute for Materials Science$B!!J*<A!&:`NA8&5f5!9=(J *
*> 1-2-1 Sengen, Tsukuba 305-0047 Japan$B$D$/$P;T_at_i8=#1!]#2!<#1(J *
*> NEJO.Hitoshi_at_nims.go.jp<NEJO.Hitoshi_at_nims.go.jp?Subject=Re:%20%20psf%20file%20for%20zeolite-water%20system>
*
*> http://www.nims.go.jp/nano-elec/ *
*> TEL:+81 29 859 2847 ext.6673 *
*> FAX:+81 29 859 2801 *
*> --------------------------------------------------- *

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On Dec 5, 2007 1:16 PM, Adam Fraser <adam.n.fraser_at_gmail.com> wrote:

> I'm trying to either build or find NAMD topology files for buckminster
> fullerene (C60).
>
> Does anyone know where I could find such files?
>
> If not, does anyone know of literature that would help me build C60?
>
> I already have a pdb of the structure... I just need accurate partial
> charges to build the topology file with. Even then, I'm not confident in
> how well this will model fullerene because I just read this:
>
> "C60 has a tendency of avoiding having double bonds within the
> pentagonal rings which makes electron delocalisation poor, and
> results in the fact that C60 is not "superaromatic". C60 behaves
> very much like an electron deficient alkene..."
> source: http://www.ch.ic.ac.uk/local/projects/unwin/Fullerenes.html
>
> I greatly appreciate any help offered,
> thank you,
> Adam
>

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