Journal
JOURNAL OF COMPUTATIONAL CHEMISTRY
Volume 43, Issue 16, Pages 1113-1119Publisher
WILEY
DOI: 10.1002/jcc.26873
Keywords
electric field; electrostatics; force fields; molecular dynamics; molecular mechanics
Categories
Funding
- National Institute of Food and Agriculture [VA-160092]
- National Institute of General Medical Sciences [R35GM133754]
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We introduce TUPA, a Python-based algorithm for calculating and analyzing electric fields in molecular simulations. We also provide a PyMOL plugin to visualize electric fields within the simulation system. The features of TUPA are demonstrated through three test cases where the electric field exerted by biomolecules helps explain biological phenomena or observed kinetics.
We introduce TUPA, a Python-based algorithm to calculate and analyze electric fields in molecular simulations. To demonstrate the features in TUPA, 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 TUPA, 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 .
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