ArticleThe journal of physical chemistry. B2010
Renormalizing SMD: the renormalization approach and its use in long time simulations and accelerated PMF calculations of macromolecules.
Article in The journal of physical chemistry. B, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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17 citing papers in PubMed.
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- How Omecamtiv Modulates Myosin Motion.Biochemistry · 2025Article
- On the Control of Directionality of Myosin.Journal of the American Chemical Society · 2024Article
- Effect of Environmental Factors on the Catalytic Activity of Intramembrane Serine Protease.Journal of the American Chemical Society · 2022Article
- Exploring the activation pathway and GProceedings of the National Academy of Sciences of the United States of America · 2020Article
- Principles and Overview of Sampling Methods for Modeling Macromolecular Structure and Dynamics.PLoS computational biology · 2016Review
- Simulating the function of sodium/proton antiporters.Proceedings of the National Academy of Sciences of the United States of America · 2015Article
- Multiscale modeling of biological functions: from enzymes to molecular machines (Nobel Lecture).Angewandte Chemie (International ed. in English) · 2014Article
- Coarse-grained simulations of the gating current in the voltage-activated Kv1.2 channel.Proceedings of the National Academy of Sciences of the United States of America · 2014Article
- Electrostatic origin of the unidirectionality of walking myosin V motors.Proceedings of the National Academy of Sciences of the United States of America · 2013Article
- Modeling and simulation of ion channels.Chemical reviews · 2012Review
- Realistic simulations of the coupling between the protomotive force and the mechanical rotation of the F0-ATPase.Proceedings of the National Academy of Sciences of the United States of America · 2012Article
- Dominant folding pathways of a WW domain.Proceedings of the National Academy of Sciences of the United States of America · 2012Article
- Article
- Paradynamics: an effective and reliable model for ab initio QM/MM free-energy calculations and related tasks.The journal of physical chemistry. B · 2011Article
- Converting structural information into an allosteric-energy-based picture for elongation factor Tu activation by the ribosome.Proceedings of the National Academy of Sciences of the United States of America · 2011Article
- Multiscale modeling of biological functions.Physical chemistry chemical physics : PCCP · 2011Review
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2 authors.
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Abstract
Simulations of long time process in condensed phases, in general, and in biomolecules, in particular, present a major challenge that cannot be overcome at present by brute force molecular dynamics (MD) approaches. This work takes the renormalization method, intruded by us sometime ago, and establishes its reliability and potential in extending the time scale of molecular simulations. The validation involves a truncated gramicidin system in the gas phase. This system is small enough to allow for very long explicit simulations and sufficiently complex to present the physics of realistic ion channels. The renormalization approach is found to be reliable and arguably presents the first approach that allows one to exploit the otherwise problematic steered molecular dynamics (SMD) treatments in quantitative and meaningful studies. It is established that we can reproduce the long time behavior of large systems by using Langevin dynamics (LD) simulations of a renormalized implicit model. This is done without spending the enormous time needed to obtain such trajectories in the explicit system. The present study also provides a promising advance in accelerated evaluation of free energy barriers. This is done by adjusting the effective potential in the implicit model to reproduce the same passage time as that obtained in the explicit model under the influence of an external force. Here having a reasonable effective friction provides a way to extract the potential of mean force (PMF) without investing the time needed for regular PMF calculations. The renormalization approach, which is illustrated here in realistic calculations, is expected to provide a major help in studies of complex landscapes and in exploring long time dynamics of biomolecules.
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