Lipid Bilayers Driven to a Wrong Lane in Molecular Dynamics Simulations by Subtle Changes in Long-Range Electrostatic Interactions
By M. Patra, Mikko Karttunen, M. Hyvönen, E. Falck, I. Vattulainen. 2004
168 citations recorded by the source corpus.
We provide compelling evidence that different treatments of electrostatic interactions in molecular dynamics simulations may dramatically affect dynamic properties of lipid bilayers. To this end, we consider a fully hydrated pure dipalmitoylphosphatidylcholine bilayer through 50-ns molecular dynamics simulations and study various dynamic properties of individual lipids in a membrane, including the velocity autocorrelation function, the lateral and rotational diffusion coefficients, and the autocorrelation function for the area per molecule. We compare the results based on the Particle-Mesh Ewald (PME) and reaction field (RF) techniques with those obtained by an approach where the electrostatic interactions are truncated at rcut = 1.8, 2.0, and 2.5 nm. We find that the overall performance of PME is very good; its results are consistent with the expected behavior. The RF method performs rather well, too, despite certain inherent problems and the fact that its results differ from those obtained by PME. Never...
Subfields: Atomic and Molecular Physics, and Optics, Molecular Biology
View Paper: https://www.semanticscholar.org/paper/078db90aa19c19b359f1b11ce7386b363899769f
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In Molecular Biology
Citations in the corpus
- CHARMM-GUI Membrane Builder for mixed bilayers and its application to yeast membranes. (2009, methodology): “The MD simulations of mixed lipid bilayers typically involve the use of NPT, or equivalently the NP( g ¼ 0)T ensembles for most force fields except for the CHARMM force field (11,12,52).”