Re: [AMBER] significance of attaching a dummy atom in smd

From: Jason Swails <jason.swails.gmail.com>
Date: Thu, 7 Aug 2014 13:52:20 -0400

On Thu, Aug 7, 2014 at 1:32 PM, Asmita Gupta <asmita4des.gmail.com> wrote:

> Dear users,
>
>
> In constant velocity steered MD simulation, we usually attach a dummy atom
> to our atom of interest (from where we want to pull the molecule
> generally)..this seems to be suggested in tutorials also..
>
> I have come across many papers in which people, however, have applied
> forces directly to the atom in the molecule of interest without attaching a
> dummy atom physically.
>
> My doubt is, how important is it to attach a dummy atom at all in such
> simulations? Does it hold any physical meaning? Will the simulation show
> any artefacts if i apply a desired force directly, say at 5' ends of DNA?
>

‚ÄčI only use a dummy atom when I _need_ to -- that is, if I'm trying to pull
along a reaction coordinate in which one of the "endpoints" does not
correspond to a physical atom (for instance, if you are trying to pull a
linear chain through a macrocycle and want to pull it away from the
macrocycle into bulk solvent). Then you can use other restraints to anchor
the dummy atom in a fixed position wrt a particular frame of reference
(rather than absolute coordinates in cartesian space).

Usually, I've been able to define a reaction coordinate using two physical
atoms, so I rarely have to deal with dummy atoms for steered MD
simulations. See, for example,
http://pubs.acs.org/doi/abs/10.1021/jp806906x.

HTH,
Jason

-- 
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Thu Aug 07 2014 - 11:00:03 PDT
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