The DOI matches its Crossref record; 38 of the 38 references it cites were found in a registry or an index.
Moltemplate: A Tool for Coarse-Grained Modeling of Complex Biological Matter and Soft Condensed Matter Physics
Open accessAbstract
Coarse-grained models have long been considered indispensable tools in the investigation of biomolecular dynamics and assembly. However, the process of simulating such models is arduous because unconventional force fields and particle attributes are often needed, and some systems are not in thermal equilibrium. Although modern molecular dynamics programs are highly adaptable, software designed for preparing all-atom simulations typically makes restrictive assumptions about the nature of the particles and the forces acting on them. Consequently, the use of coarse-grained models has remained challenging. Moltemplate is a file format for storing coarse-grained molecular models and the forces that act on them, as well as a program that converts moltemplate files into input files for LAMMPS, a popular molecular dynamics engine. Moltemplate has broad scope and an emphasis on generality. It accommodates new kinds of forces as they are developed for LAMMPS, making moltemplate a popular tool with thousands of users in computational chemistry, materials science, and structural biology. To demonstrate its wide functionality, we provide examples of using moltemplate to prepare simulations of fluids using many-body forces, coarse-grained organic semiconductors, and the motor-driven supercoiling and condensation of an entire bacterial chromosome.
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Cites
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Cited by
Thompson, A. P., Aktulga, H. M., Berger, R., Bolintineanu, D. S., Brown, W. M., Crozier, P. S., in 't Veld, P. J., Kohlmeyer, A., Moore, S. G., Nguyen, T. D., et al. (2022) · Computer Physics Communications · doi:10.1016/j.cpc.2021.108171 · Cited by 12,598
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DynaMate: Leveraging AI-agents for customized research workflows
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A Coarse-Grained MARTINI Model for Mucins
Kanesalingam, T., Weiand, E., Cann, P. M., Masen, M., & Ewen, J. P. (2026) · Journal of Chemical Theory and Computation · doi:10.1021/acs.jctc.5c01655 · Cited by 6
Metadata
- Authors
- Jewett, A. I., Stelter, D., Lambert, J., Saladi, S. M., Roscioni, O. M., Ricci, M., Autin, L., Maritan, M., Bashusqeh, S. M., Keyes, T., Dame, R. T., Shea, J.-E., Jensen, G. J., & Goodsell, D. S.
- Venue
- Journal of Molecular Biology
- Publisher
- Elsevier BV
- Published
- 2021-05
- Volume
- 433
- Issue
- 11
- Pages
- 166841
- ISSN
- 0022-2836 (ISSN-L)
- OpenAlex
- W3128698945
- Cited by
- 521
- References
- 38
- FWCI
- 20.06
- Type
- journal article
- Language
- en
- Open access
- bronze
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- Jewett, A. I., Stelter, D., Lambert, J., Saladi, S. M., Roscioni, O. M., Ricci, M., Autin, L., Maritan, M., Bashusqeh, S. M., Keyes, T., Dame, R. T., Shea, J.-E., Jensen, G. J., & Goodsell, D. S. (2021). Moltemplate: A Tool for Coarse-Grained Modeling of Complex Biological Matter and Soft Condensed Matter Physics. Journal of Molecular Biology. https://doi.org/10.1016/j.jmb.2021.166841
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