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Routine Access to Millisecond Time Scale Events with Accelerated Molecular Dynamics
Open accessAbstract
In this work, we critically assess the ability of the all-atom enhanced sampling method accelerated molecular dynamics (aMD) to investigate conformational changes in proteins that typically occur on the millisecond time scale. We combine aMD with the inherent power of graphics processor units (GPUs) and apply the implementation to the bovine pancreatic trypsin inhibitor (BPTI). A 500 ns aMD simulation is compared to a previous millisecond unbiased brute force MD simulation carried out on BPTI, showing that the same conformational space is sampled by both approaches. To our knowledge, this represents the first implementation of aMD on GPUs and also the longest aMD simulation of a biomolecule run to date. Our implementation is available to the community in the latest release of the Amber software suite (v12), providing routine access to millisecond events sampled from dynamics simulations using off the shelf hardware.
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Cited by
Salomon-Ferrer, R., Götz, A. W., Poole, D., Le Grand, S., & Walker, R. C. (2013) · Journal of Chemical Theory and Computation · doi:10.1021/ct400314y · Cited by 3,372
Self-citationPerspective: Coarse-grained models for biomolecular systems
Noid, W. G. (2013) · The Journal of Chemical Physics · doi:10.1063/1.4818908 · Cited by 893
Enhanced sampling techniques in molecular dynamics simulations of biological systems
Bernardi, R. C., Melo, M. C. R., & Schulten, K. (2015) · Biochimica et Biophysica Acta (BBA) - General Subjects · doi:10.1016/j.bbagen.2014.10.019 · Cited by 757
Improved Reweighting of Accelerated Molecular Dynamics Simulations for Free Energy Calculation
Miao, Y., Sinko, W., Pierce, L., Bucher, D., Walker, R. C., & McCammon, J. A. (2014) · Journal of Chemical Theory and Computation · doi:10.1021/ct500090q · Cited by 455
Self-citationRobichaux, J. P., Elamin, Y. Y., Vijayan, R. S. K., Nilsson, M. B., Hu, L., He, J., Zhang, F., Pisegna, M., Poteete, A., Sun, H., et al. (2019) · Cancer Cell · doi:10.1016/j.ccell.2019.09.001 · Cited by 242
Metadata
- Authors
- Pierce, L. C. T., Salomon-Ferrer, R., Augusto F. de Oliveira, C., McCammon, J. A., & Walker, R. C.
- Venue
- Journal of Chemical Theory and Computation
- Publisher
- American Chemical Society (ACS)
- Published
- 2012-08-08
- Volume
- 8
- Issue
- 9
- Pages
- 2997-3002
- ISSN
- 1549-9618 (ISSN-L)
- 1549-9626
- OpenAlex
- W1975734016
- Cited by
- 513
- References
- 0
- FWCI
- 10.46
- Type
- journal article
- Language
- en
- Open access
- hybrid
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- Pierce, L. C. T., Salomon-Ferrer, R., Augusto F. de Oliveira, C., McCammon, J. A., & Walker, R. C. (2012). Routine Access to Millisecond Time Scale Events with Accelerated Molecular Dynamics. Journal of Chemical Theory and Computation. https://doi.org/10.1021/ct300284c
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Bibliographic data: Semantic Scholar, OpenAlex, Crossref.
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.
