ABSTRACT
Any resource on membrane simulations would be incomplete if system construction were not addressed; in contrast to soluble proteins and nucleic acids, there are a number of challenges involved in building a liquid crystalline lipid bilayer and embedding a protein in it. Many phospholipids have been parametrized as part of a number of force elds and parameter databases. ese databases, such as Lipidbook (https://lipidbook.bioch.ox.ac.uk/ package/), are a good reference or starting point when you are designing a system and deciding on membrane composition. However, it is important to note that lipid force elds are still largely a work in progress and are continuously being reparametrized. Presently, three major lipid force eld families are in common use (CHARMM, Berger, and GROMOS), and it was not until the recent Lipid11 (Skjevik et al., 2012) release that Amber included welltested parameters. In this section, we will also discuss applying the canonical (number, volume, and temperature [NVT]), microcanonical (number, volume, and total energy [NVE]), and isothermal-isobaric (number, pressure, and temperature [NPT]) ensembles to membrane protein systems. Finally, various system construction methods are discussed. Several protocols exist for stably inserting the protein into the bilayer eciently. ese are important because this process can be inherently slow-it is possible to collect an entire
simulation without realizing that the protein is not properly embedded in the membrane. Correct protein placement is crucial to the validity of your simulation results.
