[AMBER] significance of attaching a dummy atom in smd

From: Asmita Gupta <asmita4des.gmail.com>
Date: Thu, 7 Aug 2014 23:02:12 +0530

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?

Thank you

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Received on Thu Aug 07 2014 - 11:00:02 PDT
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