I have run a MD simulation containing protein and water/ethanol mixture.
But, something was questionable for me.
Ethanol and water molecules were placed randomly in the box.
But, after simulation, ethanol molecules were close to the protein in the center of the box, while water molecules were shifted to the box corners.
I was not able to find any explanation for this.
Could you please tell me if you know about this?
And, does this show anything important about protein structure or unfolding of protein?
Sounds like your force field parameters are imbalanced, with ethanol acting almost like a detergent rather than remaining mixed with the water as a co-solvent. While I can’t say offhand how much phase separation should occur in a system like this, it sounds wrong.
You are right. As I read ethanol had pseudosurfactant behavior.
But, I guess this can not be a problem. As I did that simulation based on Gromacs predetermined forcefield. And dissolved protein behaved differently (unfolding) rathar than being dissolved in pure water.