ArticleJournal of chemical theory and computation2023
Neighbor List Artifacts in Molecular Dynamics Simulations.
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 45 papers.
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45 citing papers in PubMed.
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- Network pharmacology analysis and cellular experiment validation of puerarin in attenuating TBI through suppression of ferroptosis.Scientific reports · 2026Article
- Folded domains impose structural heterogeneity and attenuated dynamics in biomolecular condensates.Nature communications · 2026Article
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- Structural and functional implications of phase separation of membrane protein LacY in Escherichia coli.Nature communications · 2026Article
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- Structures of invertebrate PEZO-1 isoforms with a compact architecture and a dispensable pore-distal N-terminal blade.Cell reports · 2026Article
- Coarse-grained Martini 3 model for collagen fibrils.Biophysical journal · 2026Article
- Optimizing a coarse-grained model for large-scale membrane protein simulation.Biophysical reports · 2025Article
- Membrane Constriction by Dynamin through GTP-Driven Conformational Changes from Coarse-Grained Molecular Dynamics Simulations.The journal of physical chemistry letters · 2025Article
- MreB filaments in the elongasome modulate E. coli membrane curvature.Biophysical journal · 2025Article
- Identification of potential natural BCL-2 inhibitors for leukemia through an integrated virtual screening approach.BMC pharmacology & toxicology · 2025Article
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Molecular dynamics (MD) simulations are widely used in biophysical research. To aid nonexpert users, most simulation packages provide default values for key input parameters. In MD simulations using the GROMACS package with default parameters, we found large membranes to deform under the action of a semi-isotropically coupled barostat. As the primary cause, we identified overly short outer cutoffs and infrequent neighbor list updates that resulted in missed nonbonded interactions. Small but systematic imbalances in the apparent pressure tensor then induce unphysical asymmetric box deformations that crumple the membrane. We also observed rapid oscillations in averages of the instantaneous pressure tensor components and traced these to the use of a dual pair list with dynamic pruning. We confirmed that similar effects are present in MD simulations of neat water in atomistic and coarse-grained representations. Whereas the slight pressure imbalances likely have minimal impact in most current atomistic MD simulations, we expect their impact to grow in studies of ever-larger systems with coarse-grained representation, in particular, in combination with anisotropic pressure coupling. We present measures to diagnose problems with missed interactions and guidelines for practitioners to avoid them, including estimates for appropriate values for the outer cutoff
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.