Re: [AMBER] Dummy atom and PMEMD

From: David A Case <>
Date: Thu, 30 Aug 2012 13:04:53 -0400

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?


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Received on Thu Aug 30 2012 - 10:30:04 PDT
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