CHARMM-GUI Martini Maker for Coarse-Grained Simulations with the Martini Force Field
Open accessAbstract
Coarse-grained simulations are widely used to study large biological systems. Nonetheless, building such simulation systems becomes nontrivial, especially when membranes with various lipid types are involved. Taking advantage of the frameworks in all-atom CHARMM-GUI modules, we have developed CHARMM-GUI Martini Maker for building solution, micelle, bilayer, and vesicle systems as well as systems with randomly distributed lipids using the Martini force field. Martini Maker supports 82 lipid types and different flavors of the Martini force field, including polar and nonpolar Martini, Dry Martini, and ElNeDyn (an elastic network model for proteins). The qualities of the systems generated by Martini Maker are validated by simulations of various examples involving proteins and lipids. We expect Martini Maker to be a useful tool for modeling large, complicated biomolecular systems in a user-friendly way.
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Electropores may form under external electric fields and can also arise spontaneously in naturally occurring systems due to transient transmembrane potentials arising from bilayer-surface charge fluctuations.
“Electropores may form under external electric fields 9 and can also arise spontaneously in naturallyoccuring (particularly biological) systems due to transient transmembrane potentials arising from bilayer-surface charge flucuations 8,12,[22][23][24][25][26][27][28][29][30] .”
From Fusion of lipid membranes: an alternative pathway (2026) · cites this paper as [27]
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Self-citationMartinize2 and Vermouth provide a unified framework for molecular topology generation
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Fusion of lipid membranes: an alternative pathway
Jin, D., Li, Z., Roke, S., & Klein, J. (2026) · doi:10.64898/2026.02.19.706911
- Authors
- Qi, Y., Ingólfsson, H. I., Cheng, X., Lee, J., Marrink, S. J., & Im, W.
- Affiliations
- University of Kansas (US)
- University of Groningen (NL)
- Corresponding author
- Im, Wonpil
- Venue
- Journal of Chemical Theory and Computation
- Publisher
- American Chemical Society (ACS)
- Published
- 2015-08-27
- Volume
- 11
- Issue
- 9
- Pages
- 4486-4494
- ISSN
- 1549-9618 (ISSN-L)
- 1549-9626
- OpenAlex
- W2460255279
- Cited by
- 494
- References
- 1
- Citations by year
- 2026: 58 · 2025: 67 · 2024: 71 · 2023: 63 · 2022: 56 · 2021: 53 · 2020: 40 · 2019: 27 · 2018: 24 · 2017: 21 · 2016: 12 · 2015: 1 · 2013: 1
- FWCI
- 7.63
- Type
- journal article
- Language
- en
- Open access
- green
- research.rug.nl
- Licence
- other-oa
- Locations
- Journal of Chemical Theory and Computation (publishedVersion)
- PubMed (publishedVersion)
- University of Groningen research database (University of Groningen / Centre for Information Technology) (submittedVersion, other-oa)
- Funders
- National Science Foundation (ABI-1145987)
- Nederlandse Organisatie voor Wetenschappelijk Onderzoek
- National Institute of General Medical Sciences (U54GM087519)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Lipid Membrane Structure and Behavior
- Physical Sciences › Chemistry › Physical and Theoretical Chemistry › Advanced Physical and Chemical Molecular Interactions
- Keywords
- Martini force field, coarse-grained molecular simulation, lipid bilayers, vesicles, micelles, membrane systems, lipid type, elastic network model
- MeSH terms
- Computer Graphics, Lipids, Micelles, Proteins, Software, Molecular Dynamics Simulation
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