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

[Justin Lemkul]

On 7/17/17 2:14 PM, Nidhin Thomas wrote:
> 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'm assuming you mean restraints?  You certainly should be using constraints.

> 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.
> 

Freezing is a very severe and artificial perturbation.  It's entirely possible 
that water leaked in as an artifact of having an immobile protein.

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

Not necessarily.  I rarely find freezing necessary or appropriate.

> 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 ?
> 

Check convergence by looking at the time-dependence of any relevant property.

-Justin

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Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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