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

Erik Marklund erikm at xray.bmc.uu.se
Sat Nov 10 05:07:23 CET 2012

I second everything that Justin Lemkul  wrote. This recent paper (C. A. Brackley, M. E. Cates, and D. Marenduzzo, Phys. Rev. Lett. 109:168103 (2012)) have a few weak points in my opinion, but demonstrate the artifacts that arise from freezing the DNA.


9 nov 2012 kl. 20.42 skrev Justin Lemkul:

> 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
> -- 
> ========================================
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> ========================================
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Erik Marklund, PhD
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,    75124 Uppsala, Sweden
phone:    +46 18 471 6688        fax: +46 18 511 755
erikm at xray.bmc.uu.se

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