MembIT – A Tool to Calculate Solute Membrane Insertions and Deformations in Molecular Dynamics Simulations

Abstract

In molecular dynamics simulations of membrane systems, it is very important to evaluate the interactions between membrane bilayers and other molecules like small compounds, peptides, or proteins. When these interactions lead to local deformations in the membrane, it is essential to fully understand and accurately characterize them, since these deformations can impact the calculation of membrane properties. Here, we introduce MembIT, a simple standalone tool that calculates several membrane properties that are very useful to gauge system equilibration and quality control in molecular dynamics simulations. It has implemented a distinction between local and bulk lipids, which corrects the local deformations, that are often overlooked by other tools. We show examples of MembIT calculations of membrane insertion and deformation values in systems containing POPC and a small drug (sunitinib), a transmembrane peptide (pHLIP), and a transmembrane protein (ADP/ATP carrier). We hope that this tool will be adopted by the scientific community and that the analyses that it provides become good practices in MD simulations of membrane systems.