ArticleJournal of chemical theory and computation2024
Faster Sampling in Molecular Dynamics Simulations with TIP3P-F Water.
Article in Journal of chemical theory and computation, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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Who cites it
13 citing papers in PubMed.
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- Identification of a novel oral potential multiple agonist for obesity treatment: multi-target in silico study.Journal of computer-aided molecular design · 2026Article
- Visceral Leishmaniasis: Integrated In Silico Screening of Djiboutian Medicinal Plant Phytoconstituents TargetingPharmaceuticals (Basel, Switzerland) · 2026Article
- RSM-GA-BP optimization of Ultrasound-Enzyme-Assisted deep eutectic solvent extraction (UEADESE) for flavonoids from Abelmoschus manihot (L.) leaves and mechanistic insights.Ultrasonics sonochemistry · 2026Article
- Genomic structural equation modeling reveals shared genetic structure of cardiac function and structure-function association studies of CLCNKA mutations.Scientific reports · 2026Article
- Accelerating Replica Exchange Molecular Dynamics: A Comparison of Hydrogen Mass Repartitioning and Light Water Models.Journal of chemical theory and computation · 2026Article
- Investigating the molecular mechanisms of the "Tianma-Gouteng" herb pair in treating Parkinson's disease: a bioinformatics approach and density functional theory with molecular dynamics simulations validation.Frontiers in bioinformatics · 2026Article
- Elucidating the molecular mechanisms of paeoniflorin intervention in oral lichen planus: a computational biology and bioinformatics-based research strategy.Frontiers in bioinformatics · 2026Article
- Exploring the Potential Molecular Targets of Cyanidin-3-O-glucoside for Type 2 Diabetes Mellitus Treatment.Endocrine, metabolic & immune disorders drug targets · 2026Article
- Immunoinformatics-driven design of a multi-epitope vaccine againstFrontiers in immunology · 2026Article
- Combining Molecular Dynamics and Machine Learning to Predict Drug Resistance Causing Variants of BRAF in Colorectal Cancer.Molecules (Basel, Switzerland) · 2025Article
- Faster Sampling in Molecular Dynamics Simulations with TIP3P-F Water.Journal of chemical theory and computation · 2024Article
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The need for short time steps currently limits routine atomistic molecular dynamics (MD) simulations to the microsecond time scale. For long time steps, the numerical integration of the equations of motion becomes unstable, resulting in catastrophic crashes. Here, we combine mass repartitioning and rescaling to construct a water model that increases the sampling efficiency in biomolecular simulations without compromising integration stability and with preserved structural and thermodynamic properties. The resulting "fast water" is then used with a time step as before in combination with standard force fields. The reduced water viscosity and faster diffusion result in proportionally faster sampling of the larger-scale motions in the conformation space of both solute and solvent. We illustrate this approach by developing TIP3P-F based on the popular TIP3P model of water. A roughly 2-fold boost in the sampling efficiency at minimal cost in accuracy is substantial and helps lower the energy impact of large-scale MD simulations. The approach is general and can readily be applied to other water models and different types of solvents.
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Registered trials
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