PySAGES (Python Suite for Advanced General Ensemble Simulations)
POSTER
Abstract
Molecular Dynamics simulations are now a core component in science for understanding, prediction, and design of properties at the molecular scale, but determining the free energy of many systems requires the use of enhanced sampling techniques. In this sense, having software tools providing advanced sampling methods that can be seamlessly adapted to a broad range of complex systems is essential. Continuing with the efforts of having an open-source community supported software, we introduced PySAGES, a Python implementation of SSAGES (Software Suite for Advanced General Ensemble Simulations) with full support of GPUs for the massive parallel applications of enhanced sampling methods like adaptative forces, harmonic bias, and forward flux sampling in molecular dynamics simulations. The intuitive interface facilitates the configuration of the system, the inclusion of new collective variables, and more sophisticated free energy methods can be adapted to the software with little effort. In this work, the core features are introduced along with clear and concise examples of the capabilities of this software.
*This work was supported by MICCoM, as part of the Computational Materials Sciences Program funded by the U.S. Department of Energy, Office of Science, Basic Energy Sciences, Materials Sciences, and Engineering Division through Argonne National Laboratory.
Presenters
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Gustavo R Perez Lemus
- Pritzker School of Molecular Engineering, University of Chicago
- University of Chicago