OpenMM-UFEDMM Tutorials

OpenMM is a free, open-source MD library that operates in diverse hardware platforms, such as multi-core processors and graphics processing units (GPUs). It is highly customizable by design, distinguishing itself from other popular MD software packages. In OpenMM, implementing a new potential energy term or integration algorithm can be as simple as providing character strings with proper algebraic expressions. The program will parse these expressions, optimize and differentiate them, and generate execution kernels for the desired hardware platform. One of the handy features available in OpenMM is the CustomCVForce class, which allows the inclusion of collective variables (CVs) in the energy expression. The same customizable classes used for implementing interaction potentials are available for defining such CVs, and OpenMM will automatically apply the chain rule for computing the forces that depend on them.

We implemented a Python library that extends OpenMM to facilitate the use of extended phase-space dynamics methods for enhanced sampling of collective variables. This library, called UFEDMM, is able to launch simulations applying Unified Free Energy Dynamics (UFED),  driven Adiabatic Free Energy Dynamics or Temperature Accelerated Molecular Dynamics (d-AFED/TAMD) , metadynamics, well-tempered metadynamics, or other types of biased extended phase-space simulation. It is also flexible enough to allow the execution of related methods such as Temperature Accelerated Sliced Sampling (TASS) and d-AFED  or metadynamics with minimal extra setup effort. A repository of CVs commonly used in the study of biochemical systems, such as radius of gyration, coordination number, and helical content, is provided together with UFEDMM. 

In this tutorials we will demonstrate how to run different temperature accelerated methods using OpenMM-UFEDMM  package.