ArticleJournal of chemical theory and computation2023
Optimal Bond Constraint Topology for Molecular Dynamics Simulations of Cholesterol.
Article in Journal of chemical theory and computation, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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Who cites it
23 citing papers in PubMed.
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- Physics-based evolution of transmembrane helices reveals mechanisms of cholesterol attraction.Nature communications · 2025Article
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- Liquid-liquid phase separation of GPS2-LATS1 promotes colorectal cancer progression by reprogramming lipid metabolism.Oncogene · 2025Article
- ILVES: Accurate and Efficient Bond Length and Angle Constraints in Molecular Dynamics.Journal of chemical theory and computation · 2025Article
- LYVAC/PDZD8 is a lysosomal vacuolator.Science (New York, N.Y.) · 2025Article
- Caveolin assemblies displace one bilayer leaflet to organize and bend membranes.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
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- Caveolin assemblies displace one bilayer leaflet to organize and bend membranes.bioRxiv : the preprint server for biology · 2025Article
- Faster Sampling in Molecular Dynamics Simulations with TIP3P-F Water.Journal of chemical theory and computation · 2024Article
- CGCompiler: Automated Coarse-Grained Molecule Parametrization via Noise-Resistant Mixed-Variable Optimization.Journal of chemical theory and computation · 2023Article
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
We recently observed artificial temperature gradients in molecular dynamics (MD) simulations of phase-separating ternary lipid mixtures using the Martini 2 force field. We traced this artifact to insufficiently converged bond length constraints with typical time steps and default settings for the linear constraint solver (LINCS). Here, we systematically optimize the constraint scaffold of cholesterol. With massive virtual sites in an equimomental arrangement, we accelerate bond constraint convergence while preserving the original cholesterol force field and dynamics. The optimized model does not induce nonphysical temperature gradients even at relaxed LINCS settings and is at least as fast as the original model at the strict LINCS settings required for proper thermal sampling. We provide a python script to diagnose possible problems with constraint convergence for other molecules and force fields. Equimomental constraint topology optimization can also be used to boost constraint convergence in atomistic MD simulations of molecular systems.
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