Re: Gold nanoparticle

From: Axel Kohlmeyer (
Date: Wed Sep 25 2013 - 11:34:39 CDT

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.


> 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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