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Updated: Feb 24, 2026

Author Spotlight: Streamlining Visual Dynamics to Simplify Molecular Dynamics Simulations Using Gromacs
Published on: August 9, 2024
Molecular dynamics simulations and applications in computational toxicology and nanotoxicology
Chandrabose Selvaraj1, Sugunadevi Sakkiah1, Weida Tong1
1Division of Bioinformatics and Biostatistics, National Center for Toxicology Research, U.S. Food and Drug Administration, Jefferson, AR 72079, USA.
Abstract:
Nanotoxicology studies toxicity of nanomaterials and has been widely applied in biomedical researches to explore toxicity of various biological systems. Investigating biological systems through in vivo and in vitro methods is expensive and time taking. Therefore, computational toxicology, a multi-discipline field that utilizes computational power and algorithms to examine toxicology of biological systems, has gained attractions to scientists. Molecular dynamics (MD) simulations of biomolecules such as proteins and DNA are popular for understanding of interactions between biological systems and chemicals in computational toxicology. In this paper, we review MD simulation methods, protocol for running MD simulations and their applications in studies of toxicity and nanotechnology. We also briefly summarize some popular software tools for execution of MD simulations.
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