From: Jeffrey Potoff (jpotoff_at_chem1.eng.wayne.edu)
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
ANGLE N1 N2 N3
PATCHING FIRS NONE LAST NONE
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
> 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 <labicia_at_yahoo.it
> <mailto:labicia_at_yahoo.it>> 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
> (-) (+) (-)
> Which is the best way to do this with NAMD?
> Thanks a lot for the attention,
> best regards,
-- ====================================================================== Jeffrey J. Potoff jpotoff_at_chem1.eng.wayne.edu 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 http://potoff1.eng.wayne.edu ======================================================================
This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 05:24:14 CST