Re: Gold nanoparticle

From: Dr. Eddie (
Date: Wed Sep 25 2013 - 11:52:48 CDT

I thought the protein would be the hard part...

In the end I would like to look at effect the nanoparticles have on
ordering the system. Thus, to the best I can see right now, I would want
the course-grain model to include a local and global approximation to the
nanoparticle's electric field and surface polarizability due to water and
the proteins. I only expect the gold nanoparticle to interact via high
order electric moments, that depend on its shape, with the proteins. Is
that way off the mark?

In the end I will be trying to replicate a colleagues experimental results
of order inducement as a function of gold nanopartcile concentration and
other measures.

Thanks again!

On Wed, Sep 25, 2013 at 11:34 AM, Axel Kohlmeyer <> wrote:

> On Wed, Sep 25, 2013 at 6:25 PM, Dr. Eddie <> wrote:
> > Hi all,
> > I would like to use namd to perform a simulation with coarse-grain
> proteins
> > around gold nanoparticles. I see vmd has a coarse grain model builder so
> > that leaves the gold nanopartciles. Are there any tools for building
> these
> > nanoparticles and generating their psf using the charmm forcefield? I
> do you have an idea how you want to model / coarse grain the gold
> atoms? and how the interaction between the proteins and the gold
> particle? just having a tool to build the coarse grain model for the
> proteins, is the least of your problems.
> building custom psf files from scripting can be done with the topotools
> plugin.
> axel.
> > thought I'd ask before reinventing the wheel so to speak.
> > Thanks!
> > Eddie
> --
> Dr. Axel Kohlmeyer
> International Centre for Theoretical Physics, Trieste. Italy.


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