ArticleJournal of chemical theory and computation2011
Enhanced Lipid Diffusion and Mixing in Accelerated Molecular Dynamics.
Article in Journal of chemical theory and computation, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 43 papers.
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Who cites it
43 citing papers in PubMed.
- Coarse-Grained Simulations of Mycobacterial Outer Membranes Reveal Fluidity-Dependent PDIM Redistribution across Different Lipid Environments.Biomacromolecules · 2026Article
- Martini 3 as a Transferable Force Field for Lipopolysaccharide Parametrization.The journal of physical chemistry. B · 2026Article
- Coarse-Grained Simulations of Mycobacterial Outer Membranes Reveal Fluidity-Dependent PDIM Redistribution Across Different Lipid Environments.bioRxiv : the preprint server for biology · 2026Article
- Designing of a novel chimeric antimicrobial peptide againstResearch in pharmaceutical sciences · 2025Article
- Improved Highly Mobile Membrane Mimetic Model for Investigating Protein-Cholesterol Interactions.Journal of chemical information and modeling · 2024Article
- Investigation of nano- and microdomains formed by ceramide 1 phosphate in lipid bilayers.Scientific reports · 2023Article
- CHARMM-GUI Enhanced Sampler for various collective variables and enhanced sampling methods.Protein science : a publication of the Protein Society · 2022Article
- Binding Analysis Using Accelerated Molecular Dynamics Simulations and Future Perspectives.Advances and applications in bioinformatics and chemistry : AABC · 2022Review
- Anti-TNF Alpha Antibody Humira with pH-dependent Binding Characteristics: A constant-pH Molecular Dynamics, Gaussian Accelerated Molecular Dynamics, and In Vitro Study.Biomolecules · 2021Article
- CHARMM-GUI Supports Hydrogen Mass Repartitioning and Different Protonation States of Phosphates in Lipopolysaccharides.Journal of chemical information and modeling · 2021Article
- The intrinsically disordered N-terminus of the voltage-dependent anion channel.PLoS computational biology · 2021Article
- Dynamics and Mechanism of Binding of Androstenedione to Membrane-Associated Aromatase.Biochemistry · 2020Article
- Scalable molecular dynamics on CPU and GPU architectures with NAMD.The Journal of chemical physics · 2020Article
- Generalized Form for Finite-Size Corrections in Mutual Diffusion Coefficients of Multicomponent Mixtures Obtained from Equilibrium Molecular Dynamics Simulation.Journal of chemical theory and computation · 2020Article
- In silico identification of new inhibitors for βeta-2-glycoprotein I as a major antigen in antiphospholipid antibody syndrome.Journal of molecular modeling · 2020Article
- Location, Orientation and Aggregation of Bardoxolone-ME, CDDO-ME, in a Complex Phospholipid Bilayer Membrane.The Journal of membrane biology · 2020Article
- Accelerating Membrane Simulations with Hydrogen Mass Repartitioning.Journal of chemical theory and computation · 2019Article
- Gaussian accelerated molecular dynamics for elucidation of drug pathways.Expert opinion on drug discovery · 2018Review
- A Computational Modeling Approach Predicts Interaction of the Antifungal Protein AFP frommSphere · 2018Article
- A molecular dynamics simulation study decodes the Zika virus NS5 methyltransferase bound to SAH and RNA analogue.Scientific reports · 2018Article
Corrections and comments
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Accelerated molecular dynamics (aMD) is an enhanced sampling technique that expedites conformational space sampling by reducing the barriers separating various low-energy states of a system. Here, we present the first application of the aMD method on lipid membranes. Altogether, ∼1.5 μs simulations were performed on three systems: a pure POPC bilayer, a pure DMPC bilayer, and a mixed POPC:DMPC bilayer. Overall, the aMD simulations are found to produce significant speedup in trans-gauche isomerization and lipid lateral diffusion versus those in conventional MD (cMD) simulations. Further comparison of a 70-ns aMD run and a 300-ns cMD run of the mixed POPC:DMPC bilayer shows that the two simulations yield similar lipid mixing behaviors, with aMD generating a 2-3-fold speedup compared to cMD. Our results demonstrate that the aMD method is an efficient approach for the study of bilayer structural and dynamic properties. On the basis of simulations of the three bilayer systems, we also discuss the impact of aMD parameters on various lipid properties, which can be used as a guideline for future aMD simulations of membrane systems.
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Registered trials
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.