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

saber naderi sbrnaderi at gmail.com
Fri Nov 9 15:02:36 CET 2012

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.
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

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.

Thanks in advance,

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