Perturbation Free-Energy Toolkit: An Automated Alchemical Topology Builder
Dražen Petrov
Abstract
, with GROMOS and GROMACS simulation packages, respectively. The same relative free energies between the three states are obtained by employing the enveloping distribution sampling (EDS) approach when compared to the pairwise perturbations. Importantly, this toolkit is made available online as an open-source Python package (https://github.com/drazen-petrov/SMArt).
Topics & Concepts
Computer sciencePerturbation (astronomy)Topology (electrical circuits)Energy (signal processing)PhysicsComputational scienceMathematicsCombinatoricsQuantum mechanicsMachine Learning in Materials ScienceOrigins and Evolution of LifeCarbon Nanotubes in Composites