ArticleEuropean biophysics journal : EBJ2003
A consistent potential energy parameter set for lipids: dipalmitoylphosphatidylcholine as a benchmark of the GROMOS96 45A3 force field.
Article in European biophysics journal : EBJ, 2003. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 51 papers.
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51 citing papers in PubMed.
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- Computer simulations of protein-membrane systems.Progress in molecular biology and translational science · 2020Article
- Lipid Head Group Parameterization for GROMOS 54A8: A Consistent Approach with Protein Force Field Description.Journal of chemical theory and computation · 2019Article
- Simulation Best Practices for Lipid Membranes [Article v1.0].Living journal of computational molecular science · 2019Article
- Atomistic-level study of the interactions between hIAPP protofibrils and membranes: Influence of pH and lipid composition.Biochimica et biophysica acta. Biomembranes · 2018Article
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- Genotype-specific differences in structural features of hepatitis C virus (HCV) p7 membrane protein.Biochimica et biophysica acta · 2015Article
- Interaction of the antimicrobial peptide polymyxin B1 with both membranes of E. coli: a molecular dynamics study.PLoS computational biology · 2015Article
- Structure based computational assessment of channel properties of assembled ORF-8a from SARS-CoV.Proteins · 2015Article
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7 authors.
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Abstract
The performance of the GROMOS96 parameter set 45A3 developed for aliphatic alkanes is tested on a bilayer of dipalmitoylphosphatidylcholine (DPPC) in water in the liquid-crystalline L(alpha) phase. Variants of the force-field parameter set as well as different sets of simulation conditions or simulation parameter sets are evaluated. In the case of the force-field parameters, the van der Waals constants for the non-bonded interaction of the ester carbonyl carbon and the partial charges and charge group definition of the phosphatidylcholine head group are examined. On the methodological side, different cut-off distances for the non-bonded interactions, use of a reaction-field force due to long-range electrostatic interactions, the frequency of removal of the centre of mass motion and the strength of the coupling of the pressure of the system to the pressure bath are tested. The area per lipid, as a measure of structure, the order parameters of the chain carbons, as a measure of membrane fluidity, and the translational diffusion of the lipids in the plane of the bilayer are calculated and compared with experimental values. An optimal set of simulation parameters for which the GROMOS96 parameter set 45A3 yields a head group area, chain order parameters and a lateral diffusion coefficient in accordance with the experimental data is listed.
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