Hi All,
I have made a MD simulation with silver atoms ions attached to DNA strands.
My problem is that the silver ions (positively charged) are sticking
together very closely, which does not seem physically accurate. I used the
ff99SB force field and implicit solvent (IGB = 1).
I have attached a snapshot of the simulation after 20ns. The green spheres
represent positive silver ions and silver spheres represent neutral silver
atoms. I initialized some of the silver ions close together, but they
should have repelled. I suspect the force field or implicit solvent models
have something to do with this, but I would like to hear from you all.
Thanks,
Alex
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Received on Wed Feb 26 2014 - 17:30:03 PST
