[gmx-users] Equilibration of Lipid Bilayers created through charmm-gui

[Nidhin Thomas]

Hello  everyone,

I have created an 'alpha-helix protein embedded in a lipid bilayer’ system using charmm-gui.

I used the mdp files provided by charmm-gui directly without changing the number of steps or constraints for equilibration. I ran final simulation for 200 ns without any constraints and obtained a system in which there was no water penetration into the bilayer.

I compared my results against a research paper and I see water penetration into the bilayer for that system. They didn’t use charm-gui for modeling and they had frozen the protein during the initial equilibration compared to my system.

Should we always freeze the protein during the initial equilibration time and let lipids settle before starting the equilibration with constraints to protein?

When I used the mdp files obtained from charmm-gui directly, I checked the RMSD values of the protein and it’s within 3 Angstrom which I think is within the acceptable range. Also average protein tilt within the lipids is also constant. Could you please tell me what else I can check to confirm if my system is fully equilibrated ?

Thanks everyone,

Nidhin Thomas