On Tue, Aug 28, 2012, Ali M. Naserian-Nik wrote:
>
> Is there any way to include a dummy atom in pmemd simulations?
What do you want the dummy atom to represent? And why do you think you need
one?
It's certainly possible to define a center that has no LJ paramters (and no
charge) but is bonded to other atoms. This is what people usually mean by the
term "dummy atom". What is not clear is why you think you need it. In the
old days, dummy atoms were used for alchemical free energy calculations, but
pmemd doesn't support such calculations, (and sander doesn't require dummy
atoms any more).
....dac
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Received on Tue Aug 28 2012 - 18:00:03 PDT
