Re: nitrogen in namd

From: Jeffrey Potoff (
Date: Wed Jul 27 2011 - 15:51:57 CDT

This is pretty easy to do in NAMD. The topology looks like this:

RESI N2 0.0
ATOM N1 N -0.482
ATOM N2 Na 0.984
ATOM N3 N -0.482
BOND N1 N2 N2 N3

You just need to create a dummy site with some mass and set the LJ
parameters of 0.

On 7/27/2011 3:49 PM, Erik Nordgren wrote:
> 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?
> -Erik
> --
> 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

Jeffrey J. Potoff
Associate Professor			  Wayne State University		
Department of Chemical Engineering and Materials Science
5050 Anthony Wayne Dr			  Phone:(313)577-9357		
Detroit, MI 48202  	                  Fax:  (313)578-5815

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