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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