MDMS: Software Facilitating Performing Molecular Dynamics Simulations.

Molecular Dynamics Made Simple (MDMS) is software that facilitates performing molecular dynamics (MD) simulations of solvated protein/protein-ligand complexes with Amber, one of the most popular MD codes. It guides users through the whole process of running MD starting with choosing a protein structure, preparing the model, parametrization of the system, establishing parameters for controlling MD, and finally running simulations. By accommodating every step required for running MD, this software ensures that the simulations performed by a user will provide as realistic insight as it is possible. Its sequential structure and a text-based interface ensure ease of use, while the flexibility required for complex cases is still preserved. MDMS also provides a very time-efficient and streamlined method to start MD simulations, which makes it a feasible tool for both novices and experienced computational chemists.