The DOI matches its Crossref record; 3 of the 3 references it cites were found in a registry or an index.
A Multiscale Coarse-Graining Method for Biomolecular Systems
Abstract
A new approach is presented for obtaining coarse-grained (CG) force fields from fully atomistic molecular dynamics (MD) trajectories. The method is demonstrated by applying it to derive a CG model for the dimyristoylphosphatidylcholine (DMPC) lipid bilayer. The coarse-graining of the interparticle force field is accomplished by an application of a force-matching procedure to the force data obtained from an explicit atomistic MD simulation of the biomolecular system of interest. Hence, the method is termed a "multiscale" CG (MS-CG) approach in which explicit atomistic-level forces are propagated upward in scale to the coarse-grained level. The CG sites in the lipid bilayer application were associated with the centers-of-mass of atomic groups because of the simplicity in the evaluation of the forces acting on them from the atomistic data. The resulting CG lipid bilayer model is shown to accurately reproduce the structural properties of the phospholipid bilayer.
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Citations
Cites
Coarse Grained Model for Semiquantitative Lipid Simulations
Marrink, S. J., de Vries, A. H., & Mark, A. E. (2004) · The Journal of Physical Chemistry B · doi:10.1021/jp036508g · Cited by 2,257
Interatomic Potentials from First-Principles Calculations: The Force-Matching Method
Ercolessi, F., & Adams, J. B. (1994) · Europhysics Letters (EPL) · doi:10.1209/0295-5075/26/8/005 · Cited by 1,455
Meyer, H., Biermann, O., Faller, R., Reith, D., & Müller-Plathe, F. (2000) · The Journal of Chemical Physics · doi:10.1063/1.1308542 · Cited by 128
Cited by
Computer Simulation of Liquids
Allen, M. P., & Tildesley, D. J. (2017) · doi:10.1093/oso/9780198803195.001.0001 · Cited by 20,945
Perspective: Coarse-grained models for biomolecular systems
Noid, W. G. (2013) · The Journal of Chemical Physics · doi:10.1063/1.4818908 · Cited by 893
Coarse-Graining of Condensed Phase and Biomolecular Systems
(2008) · CRC Press eBooks · doi:10.1201/9781420059564 · Cited by 677
Multiscale simulation of soft matter systems–from the atomistic to the coarse-grained level and back
Peter, C., & Kremer, K. (2009) · Soft Matter · doi:10.1039/b912027k · Cited by 465
Lipids on the move: Simulations of membrane pores, domains, stalks and curves
Marrink, S. J., de Vries, A. H., & Tieleman, D. P. (2009) · Biochimica et Biophysica Acta (BBA) - Biomembranes · doi:10.1016/j.bbamem.2008.10.006 · Cited by 440
Metadata
- Authors
- Izvekov, S., & Voth, G. A.
- Venue
- The Journal of Physical Chemistry B
- Publisher
- American Chemical Society (ACS)
- Published
- 2005-01-22
- Volume
- 109
- Issue
- 7
- Pages
- 2469-2473
- ISSN
- 1520-5207 (ISSN-L)
- 1520-6106
- OpenAlex
- W2061308254
- Cited by
- 1,197
- References
- 3
- FWCI
- 11.98
- Type
- journal article
- Language
- en
- Open access
- closed
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Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.
