ArticleJournal of chemical theory and computation2010
Implementation of molecular dynamics and its extensions with the coarse-grained UNRES force field on massively parallel systems; towards millisecond-scale simulations of protein structure, dynamics, and thermodynamics.
Article in Journal of chemical theory and computation, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.
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Who cites it
25 citing papers in PubMed.
- Parametrization of βJournal of chemical information and modeling · 2026Article
- Recent advances in machine learning and coarse-grained potentials for biomolecular simulations.Biophysical journal · 2026Review
- Implementation of Time-Averaged Restraints with UNRES Coarse-Grained Model of Polypeptide Chains.Journal of chemical theory and computation · 2025Article
- Coarse-Grained Simulation Study of the Association of Selected Dipeptides.The journal of physical chemistry. B · 2024Article
- Assessment of Two Restraint Potentials for Coarse-Grained Chemical-Cross-Link-Assisted Modeling of Protein Structures.Journal of chemical information and modeling · 2024Article
- UNRES-GPU for physics-based coarse-grained simulations of protein systems at biological time- and size-scales.Bioinformatics (Oxford, England) · 2023Article
- Prediction of Aggregation of Biologically-Active Peptides with the UNRES Coarse-Grained Model.Biomolecules · 2022Article
- Improvements and new functionalities of UNRES server for coarse-grained modeling of protein structure, dynamics, and interactions.Frontiers in molecular biosciences · 2022Article
- Role of Glycosaminoglycans in Procathepsin B Maturation: Molecular Mechanism Elucidated by a Computational Study.Journal of chemical information and modeling · 2020Article
- Improved Consensus-Fragment Selection in Template-Assisted Prediction of Protein Structures with the UNRES Force Field in CASP13.Journal of chemical information and modeling · 2020Article
- Processing and Maturation of Cathepsin C Zymogen: A Biochemical and Molecular Modeling Analysis.International journal of molecular sciences · 2019Article
- Article
- Coarse-Grained Simulations Using a Multipolar Force Field Model.Materials (Basel, Switzerland) · 2018Article
- Implementing efficient concerted rotations using Mathematica and C codeThe European physical journal. E, Soft matter · 2018Article
- Performance of protein-structure predictions with the physics-based UNRES force field in CASP11.Bioinformatics (Oxford, England) · 2016Article
- My 65 years in protein chemistry.Quarterly reviews of biophysics · 2015Review
- A unified coarse-grained model of biological macromolecules based on mean-field multipole-multipole interactions.Journal of molecular modeling · 2014Article
- Lessons from application of the UNRES force field to predictions of structures of CASP10 targets.Proceedings of the National Academy of Sciences of the United States of America · 2013Article
- Mean-field interactions between nucleic-acid-base dipoles can drive the formation of a double helix.Physical review letters · 2013Article
- Coexistence of phases in a protein heterodimer.The Journal of chemical physics · 2012Article
Corrections and comments
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Authors and funding
6 authors.
Funding
Abstract
We report the implementation of our united-residue UNRES force field for simulations of protein structure and dynamics with massively parallel architectures. In addition to coarse-grained parallelism already implemented in our previous work, in which each conformation was treated by a different task, we introduce a fine-grained level in which energy and gradient evaluation are split between several tasks. The Message Passing Interface (MPI) libraries have been utilized to construct the parallel code. The parallel performance of the code has been tested on a professional Beowulf cluster (Xeon Quad Core), a Cray XT3 supercomputer, and two IBM BlueGene/P supercomputers with canonical and replica-exchange molecular dynamics. With IBM BlueGene/P, about 50 % efficiency and 120-fold speed-up of the fine-grained part was achieved for a single trajectory of a 767-residue protein with use of 256 processors/trajectory. Because of averaging over the fast degrees of freedom, UNRES provides an effective 1000-fold speed-up compared to the experimental time scale and, therefore, enables us to effectively carry out millisecond-scale simulations of proteins with 500 and more amino-acid residues in days of wall-clock time.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.