Re: nitrogen in namd

From: Erik Nordgren (
Date: Wed Jul 27 2011 - 14:49:04 CDT

Ciao Marco,

I haven't done that sort of thing before, but it seems like you would just
need to create a little topology file that defines your 3-particle nitrogen
"molecule" as you describe, including the two "atom" types (one type with
mass~14, one with mass=0), and then add some lines to your force-field
parameter file (to impose a rigid 180-degree angle between the 3 particles,
for example). Have you tried anything like this already? If so, did you
encounter specific problems?

Also, out of curiosity, wouldn't those charges be reversed, i.e., negative
partial charge in the middle and positive charge on the nuclei?


C. Erik Nordgren, Ph.D.
Department of Chemistry
University of Pennsylvania
On Wed, Jul 27, 2011 at 5:47 AM, Marco Sant <> wrote:
> Good morning,
> I would like to compute the self-diffusion of N2 within a porous material
> using namd.
> I need to place a point charge on each N atom plus a point charge in the
> center of mass of the N2 molecule. In other words, I need something like a
> "virtual site" or a "dummy atom" having charge but not mass and being placed
> in the center of the N2 molecule.
> shape of N2
> N---------N
> (-)  (+)  (-)
> Which is the best way to do this with NAMD?
> Thanks a lot for the attention,
> best regards,
> M&B

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