<scp>TUPÃ</scp>: Electric field analyses for molecular simulations
Marcelo D. Polêto, Justin A. Lemkul
Abstract
We introduce TUPÃ, a Python-based algorithm to calculate and analyze electric fields in molecular simulations. To demonstrate the features in TUPÃ, we present three test cases in which the orientation and magnitude of the electric field exerted by biomolecules help explain biological phenomena or observed kinetics. As part of TUPÃ, we also provide a PyMOL plugin to help researchers visualize how electric fields are organized within the simulation system. The code is freely available and can be obtained at https://mdpoleto.github.io/tupa/.
Topics & Concepts
Python (programming language)Plug-inElectric fieldComputer scienceStatistical physicsAlgorithmComputational scienceTheoretical computer scienceProgramming languagePhysicsQuantum mechanicsProtein Structure and DynamicsSpectroscopy and Quantum Chemical StudiesMass Spectrometry Techniques and Applications