Re: nitrogen in namd

From: Jim Phillips (
Date: Wed Jul 27 2011 - 15:07:25 CDT

That would be a "lone pair" in the NAMD code. You'll need to modify code
such as HomePatch::reposition_all_lonepairs() to recognize and deal with
bisector lone pairs (the position calculation is trivial of course).

For a first cut you could treat the partial charges as zero, particularly
if the partial charges for your porous material are small. I'm sure there
is a chemist on the list who will respond that this is either sufficient
or useless, but I can't guess which it would be.


On Wed, 27 Jul 2011, 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

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:57:31 CST