[gmx-users] REMD with Frozen DNA and Moving Protein

Justin Lemkul jalemkul at vt.edu
Fri Nov 9 20:42:48 CET 2012

On 11/9/12 9:02 AM, saber naderi wrote:
> Dear Gromacs Users,
> I would like to study structure of a positively charged protein in the
> vicinity of DNA. To do this, I want to perform replica exchange molecular
> dynamics simulations in which DNA is frozen and only the protein moves.
> This way I can efficiently obtain the free energy landscape of the protein
> close to [frozen] DNA.
> The reason why I keep the DNA frozen is that this may reduce the
> computational cost in two ways:
> 1. DNA atom coordinates are not updated.

Frozen groups do not improve performance.

> 2. Maybe I can have a smaller simulation box (and less number of water
> molecules), because in principle I can exclude DNA-DNA interactions via
> energygrp_excl.

This is also not true, as there are protein-DNA and protein-water interactions 
that cannot be ignored.

> so, I would like to ask you if you think this is a reasonable approach?
> What could go wrong in such simulations? Any input would be appreciated.

Are you sure that there is no potential for the protein to induce any structural 
change in the DNA?  If you freeze the DNA, you assume that no remodeling occurs. 
  This assumption could impact the calculated free energy of binding.



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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