Is it possible to use umbrella sampling to simulate the complex membrane model?

User discussions
1

GROMACS version: 2021.2

Hi
I need to make some natural pore in the membrane model that contains the different types of lipids (with an asymmetric lipid distribution between the bilayer leaflets) for studying change in these pores under special conditions. I have never done umbrella sampling and I don’t know about that. But I studied some articles that simulated the membrane containing one type of lipid to investigate pore formation. Is it possible to use umbrella sampling for such complex membrane models? Because all of the articles that I studied had a pure membrane I was confused. (Just I find out the reaction coordinates are important and I don’t know that I can define them when I have different types of lipids in the membrane)

I would be grateful if you could explain this.

2

Umbrella sampling is a technique to compute a potential of mean force, not for making pores in a membrane. A complex membrane is no problem at all for most techniques.
You don’t say anything about the conditions and process of pore formation you want to study. In general it is usually a good strategy to mimic the experimental conditions in a simulation.

4

Thanks for your response. I will study more about this technique.
I thought by applying bias potentials during an umbrella sampling run I can move phospholipids into the center of the membrane (I find out in umbrella sampling I can pull phospholipids and compute the free energy for moving phospholipids.) Is it true?

5

Yes, but that would be called steered MD using an umbrella potential, not umbrella sampling.

6

Thank you