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

[saber naderi]

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
energygrp_excl.

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,
Saber