TUPÃ: Electric field analyses for molecular simulations
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Updated: Sep 26, 2025

Spatial Separation of Molecular Conformers and Clusters
Published on: January 9, 2014
Marcelo D Polêto1,2, Justin A Lemkul1,2
1Department of Biochemistry, Virginia Tech, Blacksburg, Virginia, USA.
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/.
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