ArticleMolecular simulation2009
Novel procedure for thermal equilibration in molecular dynamics simulation.
Article in Molecular simulation, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 3 papers.
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Who cites it
3 citing papers in PubMed.
- Structural and Antioxidant Comparison Between Native WPI and WPI-Resveratrol Non-Covalent Complex.Antioxidants (Basel, Switzerland) · 2026Article
- A Comparative Molecular Dynamics Study of Food-Derived Compounds as PD-L1 Inhibitors: Insights Across Six Flavonoid Subgroups.Molecules (Basel, Switzerland) · 2025Article
- Computational Screening of IL-1 and IL-6 Inhibitors for Rheumatoid Arthritis: Insights from Molecular Docking and Dynamics Analysis.Current pharmaceutical design · 2025Article
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Authors and funding
7 authors.
Funding
Abstract
We describe a simple novel procedure for achieving thermal equilibration between a protein and a surrounding solvent during molecular dynamics (MD) simulation. The method uniquely defines the length of simulation time required to achieve thermal equilibrium over a broad range of parameters, thus removing ambiguities associated with the traditional heuristic approaches. The proposed protocol saves simulation time and avoids bias introduced by the inclusion of non-equilibrium events. The key element of the procedure involves coupling only the solvent atoms to a standard heat bath. Measuring progress towards thermal equilibration involves simply monitoring the difference in temperature between the solvent and the protein. Here, we report that the results of MD simulations using the above procedure are measurably improved relative to the traditional approaches in terms of root-mean-square deviations and principal components analysis both indicating significantly less undesirable divergence.
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