From: Axel Kohlmeyer (
Date: Mon Feb 01 2016 - 01:47:00 CST

On Mon, Feb 1, 2016 at 8:29 AM, Shubham Mishra <> wrote:
> Greetings,
> I am trying to create a sphere of diameter in nanometers range representing
> a nanoparticle in a simulation. I tried graphic tools of VMD and I am
> obtaining a sphere as required using sphere command but I am not sure how to
> give properties of a particle viz. mass and degrees of freedom.

to what purpose. VMD is a visualization tool and does no computations
or needs to know these properties for anything.
you can set particle/atom masses via the script interface, but that
has no effect outside of being used for mass weighted analysis.

that said, a graphics object is just that, graphics. it has no
properties outside its drawing properties and is not part of any
molecular structure.

> I need to simulate a nanoparticle covered with a monolayer of polymeric
> capping agent and I don't require effect of material properties of
> nanoparticle at the current stage. So I don't want to use nanoparticle
> builders as mentioned in DISCUS or OpenMD and simulate the nanoparticle as a
> macromloecule.
> If there is any possible way to achieve this on VMD, if so some insight
> would be much appreciated.

you *will* need to use some kind of molecular builder that creates an
input for your simulation software.
whether you model your nanoparticle with explicit atoms or via
immobilizing atoms of your monolayer, is up to you and has to be done
according to the software you are going to use for your simulation.
VMD has very little to offer for this purpose.


> Regards,
> Shubham Mishra

Dr. Axel Kohlmeyer
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.