Re: [AMBER] Dummy atom and PMEMD

From: Ali M. Naserian-Nik <>
Date: Wed, 29 Aug 2012 10:27:06 +0430

Dear Prof. Case,

Thank you very much for your reply. In fact, I want to use two non-bonded
dummy atoms. I employ the dummy to perform steered MD simulations in a
defined direction (applying mechanical force to a DNA molecule in a certain
direction). In addition, I have used a dummy atom to construct a model, by
tleap, in which the DNA is not located at center of water box. Would you
please guide me more? Please let me know If more information is needed.

Best regards,

On Wed, Aug 29, 2012 at 5:05 AM, case <> wrote:

> 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
> _______________________________________________
> AMBER mailing list
AMBER mailing list
Received on Tue Aug 28 2012 - 23:00:04 PDT
Custom Search