From: Marco Sant (labicia_at_yahoo.it)
Date: Wed Jul 27 2011 - 04:47:15 CDT
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,
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