The DOI matches its Crossref record; 61 of the 61 references it cites were found in a registry or an index.
GPU-Accelerated Molecular Dynamics and Free Energy Methods in Amber18: Performance Enhancements and New Features
Open accessAbstract
We report progress in graphics processing unit (GPU)-accelerated molecular dynamics and free energy methods in Amber18. Of particular interest is the development of alchemical free energy algorithms, including free energy perturbation and thermodynamic integration methods with support for nonlinear soft-core potential and parameter interpolation transformation pathways. These methods can be used in conjunction with enhanced sampling techniques such as replica exchange, constant-pH molecular dynamics, and new 12-6-4 potentials for metal ions. Additional performance enhancements have been made that enable appreciable speed-up on GPUs relative to the previous software release.
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He, X., Man, V. H., Yang, W., Lee, T.-S., & Wang, J. (2020) · The Journal of Chemical Physics · doi:10.1063/5.0019056 · Cited by 783
Self-citationDeePMD-kit v2: A software package for deep potential models
Zeng, J., Zhang, D., Lu, D., Mo, P., Li, Z., Chen, Y., Rynik, M., Huang, L., Li, Z., Shi, S., et al. (2023) · The Journal of Chemical Physics · doi:10.1063/5.0155600 · Cited by 614
Self-citationLarge-Scale Assessment of Binding Free Energy Calculations in Active Drug Discovery Projects
Schindler, C. E. M., Baumann, H., Blum, A., Böse, D., Buchstaller, H.-P., Burgdorf, L., Cappel, D., Chekler, E., Czodrowski, P., Dorsch, D., et al. (2020) · Journal of Chemical Information and Modeling · doi:10.1021/acs.jcim.0c00900 · Cited by 303
Parameterization of Monovalent Ions for the OPC3, OPC, TIP3P-FB, and TIP4P-FB Water Models
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Metadata
- Authors
- Lee, T.-S., Cerutti, D. S., Mermelstein, D., Lin, C., LeGrand, S., Giese, T. J., Roitberg, A., Case, D. A., Walker, R. C., & York, D. M.
- Venue
- Journal of Chemical Information and Modeling
- Publisher
- American Chemical Society (ACS)
- Published
- 2018-09-10
- Volume
- 58
- Issue
- 10
- Pages
- 2043-2050
- ISSN
- 1549-9596 (ISSN-L)
- 1549-960X
- OpenAlex
- W2891791233
- Cited by
- 481
- References
- 61
- FWCI
- 18.11
- Type
- journal article
- Language
- en
- Open access
- green
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- Lee, T.-S., Cerutti, D. S., Mermelstein, D., Lin, C., LeGrand, S., Giese, T. J., Roitberg, A., Case, D. A., Walker, R. C., & York, D. M. (2018). GPU-Accelerated Molecular Dynamics and Free Energy Methods in Amber18: Performance Enhancements and New Features. Journal of Chemical Information and Modeling. https://doi.org/10.1021/acs.jcim.8b00462
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