Relaxing a Membrane-Containing Model System

relaxation protocol

Simulations of systems that contain membranes require some special consideration. This is because nearly all current all-atom membrane potential models in existence do not, on their own, maintain the appropriate surface areas on the time scale of tens of ns in simulations of pure membranes. If non-lipid components make up a significant fraction of the membrane region (such as a protein in a relatively small amount of lipid), this issue is much less pronounced and may not require special treatment. In this case the semi-isotropic NPT ensemble may work well. However, if the simulated membrane is pure or only contains a small solute (e.g. ligand-sized) the following practical approach may be useful.

It can be difficult to relax newly built protein-membrane systems. In particular, penetration of the water between the protein than the lipids can be problematic and require very lengthy simulations to correct. A relaxation protocol that should reduce or eliminate such problems is available in all of the Desmond panels (Molecular Dynamics Panel, Simulated Annealing Panel, Replica Exchange Panel, Metadynamics Panel), or by running the script relax_membrane.py from the command line (see Desmond Utilities).

When a membrane system is loaded into one of the panels, it automatically detects the presence of a membrane, and changes the default ensemble to NPγT and selects the Relax membrane model system before simulationoption. This makes sure that the membrane relaxation protocol is carried out before the simulation: the .msj file that is written out in the job folder includes the membrane relaxation protocol before the simulation. The relaxation protocol that is included in the distribution is used by default. You can specify a different protocol by entering the file name in the Relaxation protocol text box, or clicking Browse to locate the file.

The stages in the default membrane relaxation protocol are given below. The default thermostat (Nosé-Hoover) and barostat (Martyna-Tobias-Klein) are used throughout, as appropriate to the ensemble. From stages 2 to 4, a Gaussian biasing force is applied so that the waters do not permeate the membrane. This biasing force is not applied to crystal waters, in order to maintain their relative positions with respect to the protein.

Simulate in the NVT ensemble using Brownian dynamics with:
- a simulation time of 50ps
- a temperature of 10K
- restraints on the solute with force constant 50 kcal mol⁻¹ Å⁻².
Simulate in the NVT ensemble using Brownian dynamics with:
- a simulation time of 20ps
- a temperature of 100K
- a pressure of 1000 bar
- restraints on the solute and membrane heavy atoms with force constant 50 kcal mol⁻¹ Å⁻².
Simulate in the NPγT ensemble with:
- a simulation time of 100ps
- a temperature of 100K
- a pressure of 1000 bar
- restraints on the solute heavy atoms with force constant 10 kcal mol⁻¹ Å⁻².
- restraints on the membrane N and P atoms in the z direction with force constant 2 kcal mol⁻¹ Å⁻².
Simulate in the NPγT ensemble with:
- a simulation time of 150ps
- heating from a temperature of 100K to 300K
- a pressure of 100 bar
- restraints on the solute heavy atoms with force constant 10 kcal mol⁻¹ Å⁻².
- restraints on the membrane N and P atoms in the z direction with force constant 2 kcal mol⁻¹ Å⁻².
- restraints gradually reduced to 0.
Simulate in the NVT ensemble with:
- a simulation time of 50ps
- a temperature of 300K
- restraints on the protein backbone and the ligand heavy atoms with force constant 5 kcal mol⁻¹ Å⁻².
Simulate in the NVT ensemble with:
- a simulation time of 50ps
- a temperature of 300K
- no restraints.