Re: [AMBER] Dummy atom and PMEMD

From: Ali M. Naserian-Nik <>
Date: Thu, 30 Aug 2012 22:59:31 +0430

I have tried to perform SMD simulations with the aid of the dummy atoms
using pmemd but, as you said too, normally pmemd calculations does not
support the dummy atom and the simulation did not proceed with error. I am
searching a way that enables me to use the dummy atom within pmemd
simulations. In this way, the SMD simulations in a defined direction would
be possible by pmemd calculations, which can be ran on GPU too.

On Thu, Aug 30, 2012 at 9:34 PM, David A Case <>wrote:

> On Wed, Aug 29, 2012, Ali M. Naserian-Nik wrote:
> >
> >
> > 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.
> It sounds like you know a lot about dummy atoms, and have already used
> them in
> tleap and in doing steered MD. What is not clear is what guidance you are
> looking for. In particular, why are you asking about pmemd? Did you try
> to
> run some pmemd calculation and encounter problems?
> ...dac
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Received on Thu Aug 30 2012 - 12:00:03 PDT
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