ArticleJournal of chemical theory and computation2011
MSCALE: A General Utility for Multiscale Modeling.
Article in Journal of chemical theory and computation, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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Who cites it
20 citing papers in PubMed.
- CHARMM at 45: Enhancements in Accessibility, Functionality, and Speed.The journal of physical chemistry. B · 2024Review
- Review
- Exploring Routes to Enhance the Calculation of Free Energy Differences via Non-Equilibrium Work SQM/MM Switching Simulations Using Hybrid Charge Intermediates between MM and SQM Levels of Theory or Non-Linear Switching Schemes.Molecules (Basel, Switzerland) · 2023Article
- Optimizing the Calculation of Free Energy Differences in Nonequilibrium Work SQM/MM Switching Simulations.The journal of physical chemistry. B · 2022Article
- Use of Interaction Energies in QM/MM Free Energy Simulations.Journal of chemical theory and computation · 2019Article
- The Good, the Bad, and the Ugly: "HiPen", a New Dataset for Validating (S)QM/MM Free Energy Simulations.Molecules (Basel, Switzerland) · 2019Article
- Accelerating QM/MM Free Energy Computations via Intramolecular Force Matching.Journal of chemical theory and computation · 2018Article
- Tinker 8: Software Tools for Molecular Design.Journal of chemical theory and computation · 2018Article
- Adaptive QM/MM for Molecular Dynamics Simulations: 5. On the Energy-Conserved Permuted Adaptive-Partitioning Schemes.Molecules (Basel, Switzerland) · 2018Article
- The free energy of locking a ring: Changing a deoxyribonucleoside to a locked nucleic acid.Journal of computational chemistry · 2017Article
- LICHEM: A QM/MM program for simulations with multipolar and polarizable force fields.Journal of computational chemistry · 2016Article
- Comparison of Methods To Reweight from Classical Molecular Simulations to QM/MM Potentials.Journal of chemical theory and computation · 2016Article
- Computational scheme for pH-dependent binding free energy calculation with explicit solvent.Protein science : a publication of the Protein Society · 2016Article
- ProBiS-CHARMMing: Web Interface for Prediction and Optimization of Ligands in Protein Binding Sites.Journal of chemical information and modeling · 2015Article
- Correcting for the free energy costs of bond or angle constraints in molecular dynamics simulations.Biochimica et biophysica acta · 2015Article
- Hydrophobic hydration and the anomalous partial molar volumes in ethanol-water mixtures.The Journal of chemical physics · 2015Article
- Constant pH Molecular Dynamics in Explicit Solvent with Enveloping Distribution Sampling and Hamiltonian Exchange.Journal of chemical theory and computation · 2014Article
- Multiscale Free Energy Simulations: An Efficient Method for Connecting Classical MD Simulations to QM or QM/MM Free Energies Using Non-Boltzmann Bennett Reweighting Schemes.Journal of chemical theory and computation · 2014Article
- Enhanced Sampling in Free Energy Calculations: Combining SGLD with the Bennett's Acceptance Ratio and Enveloping Distribution Sampling Methods.Journal of chemical theory and computation · 2012Article
- Simulation of multiphase systems utilizing independent force fields to control intraphase and interphase behavior.Journal of computational chemistry · 2012Article
Corrections and comments
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Authors and funding
7 authors.
Funding
Abstract
The combination of theoretical models of macromolecules that exist at different spatial and temporal scales has become increasingly important for addressing complex biochemical problems. This work describes the extension of concurrent multiscale approaches, introduces a general framework for carrying out calculations, and describes its implementation into the CHARMM macromolecular modeling package. This functionality, termed MSCALE, generalizes both the additive and subtractive multiscale scheme (e.g. QM/MM ONIOM-type), and extends its support to classical force fields, coarse grained modeling (e.g. ENM, GNM, etc.), and a mixture of them all. The MSCALE scheme is completely parallelized with each subsystem running as an independent, but connected calculation. One of the most attractive features of MSCALE is the relative ease of implementation using the standard MPI communication protocol. This allows external access to the framework and facilitates the combination of functionality previously isolated in separate programs. This new facility is fully integrated with free energy perturbation methods, Hessian based methods, and the use of periodicity and symmetry, which allows the calculation of accurate pressures. We demonstrate the utility of this new technique with four examples; (1) subtractive QM/MM and QM/QM calculations; (2) multi-force field alchemical free energy perturbation; (3) integration with the SANDER module of AMBER and the TINKER package to gain access to potentials not available in CHARMM; and (4) mixed resolution (i.e. coarse grain / all-atom) normal mode analysis. The potential of this new tool is clearly established and in conclusion an interesting mathematical problem is highlighted and future improvements are proposed.
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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.