Moleculewise semi-grand canonical ensembles

ABSTRACT The plasma membrane is the interface between cells and exterior media. While its existence has been known for a long time, organization of its constituent lipids remain a challenge. Recently, we have proposed that lipid populations may be controlled by chemical potentials of different lipid species, resulting in semi-grand canonical thermodynamic ensembles. However, the currently available molecular dynamics software packages do not allow for molecule-based chemical potentials. Here, we propose a variation on existing algorithms that allow defining chemical potentials for molecules. Additionally, we allow coupling with collective variables and show that it can be used to dynamically create asymmetric membranes. We release an implementation of the algorithm for the HOOMD-Blue molecular dynamics engine. SIGNIFICANCE We demonstrate an algorithm that allows for simulations of molecules in the semi-grand canonical ensemble. It also allows coupling the chemical potential values to collective variable and create asymmetric membranes.