From: Ana Celia Vila Verde (
Date: Mon Feb 01 2016 - 01:55:14 CST

Dear Shubham,

The sphere command is for drawing, not for setting up the initial
configuration for a simulation.

If you need to simulate a nanoparticle covered with polymers, then I
recommend you use a nanoparticle builder. VMD is not the best tool for
this job. I've never used the nanoparticle builder tools myself but
it's possible that some of them even allow you to create a nanoparticle
covered with polymers. I guess you can also make the particle hollow so
you don't waste time simulating the inner atoms of the nanoparticle, if
it makes a big difference in the total number of atoms. If you do this,
you'll need to think of a potential that enforces the nanoparticle shape.

I hope it helps,


On 01/02/16 08:29, 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.
> 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.
> Regards,
> Shubham Mishra