Re: [AMBER] Dummy atom and PMEMD

From: Jason Swails <>
Date: Thu, 30 Aug 2012 14:48:05 -0400

On Thu, Aug 30, 2012 at 2:29 PM, Ali M. Naserian-Nik

> 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.

Why can't you just add the dummy atoms to the topology file? You could
actually do this with ParmEd. Add some ions where you want your dummy
atoms, then use to remove the charge, the van der waals terms,
and create whatever bonds you want between the system and the dummy atom
with whatever force constant you want. You can also change the mass and
atom name/type, as well. The GUI interface as well as the
manual should provide all the help you need to get started.


Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
AMBER mailing list
Received on Thu Aug 30 2012 - 12:00:03 PDT
Custom Search