Rapid exploration of configuration space with diffusion-map-directed molecular dynamics
Open accessAbstract
The gap between the time scale of interesting behavior in macromolecular systems and that which our computational resources can afford often limits molecular dynamics (MD) from understanding experimental results and predicting what is inaccessible in experiments. In this paper, we introduce a new sampling scheme, named diffusion-map-directed MD (DM-d-MD), to rapidly explore molecular configuration space. The method uses a diffusion map to guide MD on the fly. DM-d-MD can be combined with other methods to reconstruct the equilibrium free energy, and here, we used umbrella sampling as an example. We present results from two systems: alanine dipeptide and alanine-12. In both systems, we gain tremendous speedup with respect to standard MD both in exploring the configuration space and reconstructing the equilibrium distribution. In particular, we obtain 3 orders of magnitude of speedup over standard MD in the exploration of the configurational space of alanine-12 at 300 K with DM-d-MD. The method is reaction coordinate free and minimally dependent on a priori knowledge of the system. We expect wide applications of DM-d-MD to other macromolecular systems in which equilibrium sampling is not affordable by standard MD.
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Diffusion maps have been used for adaptive exploration of conformation space along slow-process eigenfunctions.
“Diffusion maps have been used for adaptive exploration of the conformation space along the slow-process eigenfunctions [11].”
From Markov state models of biomolecular conformational dynamics (2014) · cites this paper as [11]
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- Authors
- Zheng, W., Rohrdanz, M. A., & Clementi, C.
- Affiliations
- Rice University (US)
- Corresponding author
- Clementi, Cecilia
- Venue
- The Journal of Physical Chemistry B
- Publisher
- American Chemical Society (ACS)
- Published
- 2013-08-07
- Volume
- 117
- Issue
- 42
- Pages
- 12769-12776
- ISSN
- 1520-5207 (ISSN-L)
- 1520-6106
- PMC
- PMC3808479
- OpenAlex
- W2167077362
- Cited by
- 86
- References
- 27
- Citations by year
- 2026: 1 · 2025: 8 · 2023: 8 · 2022: 8 · 2021: 8 · 2020: 5 · 2019: 8 · 2018: 6 · 2017: 11 · 2016: 7 · 2015: 8 · 2014: 7 · 2013: 1
- FWCI
- 3.44
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Locations
- The Journal of Physical Chemistry B (publishedVersion)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- Rice Research Repository (Rice University) (acceptedVersion)
- Rice Research Repository (Rice University) (submittedVersion)
- Funders
- National Institutes of Health (1s10rr002950-01)
- National Center for Research Resources (S10RR029501, S10RR02950)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
- Physical Sciences › Chemistry › Physical and Theoretical Chemistry › Advanced Physical and Chemical Molecular Interactions
- Physical Sciences › Computer Science › Computational Theory and Mathematics › Computational Drug Discovery Methods
- Keywords
- configuration space exploration, umbrella sampling, alanine dipeptide
- MeSH terms
- Alanine, Diffusion, Dipeptides, Hydrogen Bonding, Temperature, Thermodynamics, Protein Folding, Molecular Dynamics Simulation
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