Re: psf file for zeolite-water system

From: Fangqiang Zhu (fzhu_at_ks.uiuc.edu)
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
> http://www.nims.go.jp/nano-elec/
> TEL:+81 29 859 2847 ext.6673
> FAX:+81 29 859 2801
> ---------------------------------------------------

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