Introducing A Software Package For The Simulation Of Biomacromolecules Using The ABSINTH Implicit Solvation Model

Computer simulations of biomolecules offer detailed insight into the molecular driving forces and mechanisms of fundamental biological processes such as protein folding or aggregation. This insight is accompanied by two major caveats, i) how authentic is the description of the system by the chosen model, and ii) how reliable are the data obtained in a statistical sense, i.e., what is the quality of sampling.The ABSINTH model, published recently (Vitalis & Pappu, J. Comput. Chem., 2008, DOI 10.1.1002/jcc.21005) tries to satisfy the second concern by coarse-graining of the solvent degrees of freedom. This leads to considerable speed-up of the simulations and allows for the study of hitherto inaccessible length and timescales in silico. Furthermore, ABSINTH has been shown to satisfy the first concern well, as a careful calibration with respect to various pieces of experimental data on relevant systems has been carried out.Here, we present the software package our laboratory has developed to study biological systems using the ABSINTH model primarily via a Monte Carlo sampling approach. We lay out the strategies employed to achieve maximal sampling quality given the challenging nature of the systems we study with finite computational resources. In addition, we provide a brief overview of the many options the program offers, which will make it a user-friendly and flexible tool that could become an important addition to the existing suite of packages and tools for the molecular simulation community. The software package will be freely available under a public license (open-source) and is not tied to any commercial interests whatsoever. To further make the case for ABSINTH, we will present new calibration results on a range of complex systems obtained using the ABSINTH paradigm.