Recent advances in QM/MM free energy calculations using reference potentials
Recent years have seen enormous progress in the development of methods for modeling (bio)molecular systems. This has allowed for the simulation of ever larger and more complex systems. However, as such complexity increases, the requirements needed for these models to be accurate and physically meani...
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| Published in | Biochimica et biophysica acta Vol. 1850; no. 5; pp. 954 - 965 |
|---|---|
| Main Authors | , , , |
| Format | Journal Article |
| Language | English |
| Published |
Netherlands
Elsevier B.V
01.05.2015
Elsevier Pub. Co |
| Subjects | |
| Online Access | Get full text |
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| Abstract | Recent years have seen enormous progress in the development of methods for modeling (bio)molecular systems. This has allowed for the simulation of ever larger and more complex systems. However, as such complexity increases, the requirements needed for these models to be accurate and physically meaningful become more and more difficult to fulfill. The use of simplified models to describe complex biological systems has long been shown to be an effective way to overcome some of the limitations associated with this computational cost in a rational way.
Hybrid QM/MM approaches have rapidly become one of the most popular computational tools for studying chemical reactivity in biomolecular systems. However, the high cost involved in performing high-level QM calculations has limited the applicability of these approaches when calculating free energies of chemical processes. In this review, we present some of the advances in using reference potentials and mean field approximations to accelerate high-level QM/MM calculations. We present illustrative applications of these approaches and discuss challenges and future perspectives for the field.
The use of physically-based simplifications has shown to effectively reduce the cost of high-level QM/MM calculations. In particular, lower-level reference potentials enable one to reduce the cost of expensive free energy calculations, thus expanding the scope of problems that can be addressed.
As was already demonstrated 40years ago, the usage of simplified models still allows one to obtain cutting edge results with substantially reduced computational cost. This article is part of a Special Issue entitled Recent developments of molecular dynamics.
•We present some of the advances to accelerate high-level QM/MM calculations.•Quantitative limitations of low-level methods can be overcome by these approaches.•Reference potentials make free energy simulations feasible for large systems.•Automated fitting reduces the need of expensive sampling of high-level approaches.•Application of reference potentials can be extended to a wide range of processes. |
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| AbstractList | Recent years have seen enormous progress in the development of methods for modeling (bio)molecular systems. This has allowed for the simulation of ever larger and more complex systems. However, as such complexity increases, the requirements needed for these models to be accurate and physically meaningful become more and more difficult to fulfill. The use of simplified models to describe complex biological systems has long been shown to be an effective way to overcome some of the limitations associated with this computational cost in a rational way.Hybrid QM/MM approaches have rapidly become one of the most popular computational tools for studying chemical reactivity in biomolecular systems. However, the high cost involved in performing high-level QM calculations has limited the applicability of these approaches when calculating free energies of chemical processes. In this review, we present some of the advances in using reference potentials and mean field approximations to accelerate high-level QM/MM calculations. We present illustrative applications of these approaches and discuss challenges and future perspectives for the field.The use of physically-based simplifications has shown to effectively reduce the cost of high-level QM/MM calculations. In particular, lower-level reference potentials enable one to reduce the cost of expensive free energy calculations, thus expanding the scope of problems that can be addressed.As was already demonstrated 40years ago, the usage of simplified models still allows one to obtain cutting edge results with substantially reduced computational cost. This article is part of a Special Issue entitled Recent developments of molecular dynamics. Recent years have seen enormous progress in the development of methods for modeling (bio)molecular systems. This has allowed for the simulation of ever larger and more complex systems. However, as such complexity increases, the requirements needed for these models to be accurate and physically meaningful become more and more difficult to fulfill. The use of simplified models to describe complex biological systems has long been shown to be an effective way to overcome some of the limitations associated with this computational cost in a rational way. Hybrid QM/MM approaches have rapidly become one of the most popular computational tools for studying chemical reactivity in biomolecular systems. However, the high cost involved in performing high-level QM calculations has limited the applicability of these approaches when calculating free energies of chemical processes. In this review, we present some of the advances in using reference potentials and mean field approximations to accelerate high-level QM/MM calculations. We present illustrative applications of these approaches and discuss challenges and future perspectives for the field. The use of physically-based simplifications has shown to effectively reduce the cost of high-level QM/MM calculations. In particular, lower-level reference potentials enable one to reduce the cost of expensive free energy calculations, thus expanding the scope of problems that can be addressed. As was already demonstrated 40years ago, the usage of simplified models still allows one to obtain cutting edge results with substantially reduced computational cost. This article is part of a Special Issue entitled Recent developments of molecular dynamics. •We present some of the advances to accelerate high-level QM/MM calculations.•Quantitative limitations of low-level methods can be overcome by these approaches.•Reference potentials make free energy simulations feasible for large systems.•Automated fitting reduces the need of expensive sampling of high-level approaches.•Application of reference potentials can be extended to a wide range of processes. • We present some of the advances to accelerate high-level QM/MM calculations. • Quantitative limitations of low-level methods can be overcome by these approaches. • Reference potentials make free energy simulations feasible for large systems. • Automated fitting reduces the need of expensive sampling of high-level approaches. • Application of reference potentials can be extended to a wide range of processes. Background: Recent years have seen enormous progress in the development of methods for modeling (bio)molecular systems. This has allowed for the simulation of ever larger and more complex systems. However, as such complexity increases, the requirements needed for these models to be accurate and physically meaningful become more and more difficult to fulfill. The use of simplified models to describe complex biological systems has long been shown to be an effective way to overcome some of the limitations associated with this computational cost in a rational way. Scope of review: Hybrid QM/MM approaches have rapidly become one of the most popular computational tools for studying chemical reactivity in biomolecular systems. However, the high cost involved in performing high-level QM calculations has limited the applicability of these approaches when calculating free energies of chemical processes. In this review, we present some of the advances in using reference potentials and mean field approximations to accelerate high-level QM/MM calculations. We present illustrative applications of these approaches and discuss challenges and future perspectives for the field. Major conclusions: The use of physically-based simplifications has shown to effectively reduce the cost of high-level QM/MM calculations. In particular, lower-level reference potentials enable one to reduce the cost of expensive free energy calculations, thus expanding the scope of problems that can be addressed. General significance: As was already demonstrated 40 years ago, the usage of simplified models still allows one to obtain cutting edge results with substantially reduced computational cost. This article is part of a Special Issue entitled Recent developments of molecular dynamics. Recent years have seen enormous progress in the development of methods for modeling (bio)molecular systems. This has allowed for the simulation of ever larger and more complex systems. However, as such complexity increases, the requirements needed for these models to be accurate and physically meaningful become more and more difficult to fulfill. The use of simplified models to describe complex biological systems has long been shown to be an effective way to overcome some of the limitations associated with this computational cost in a rational way.BACKGROUNDRecent years have seen enormous progress in the development of methods for modeling (bio)molecular systems. This has allowed for the simulation of ever larger and more complex systems. However, as such complexity increases, the requirements needed for these models to be accurate and physically meaningful become more and more difficult to fulfill. The use of simplified models to describe complex biological systems has long been shown to be an effective way to overcome some of the limitations associated with this computational cost in a rational way.Hybrid QM/MM approaches have rapidly become one of the most popular computational tools for studying chemical reactivity in biomolecular systems. However, the high cost involved in performing high-level QM calculations has limited the applicability of these approaches when calculating free energies of chemical processes. In this review, we present some of the advances in using reference potentials and mean field approximations to accelerate high-level QM/MM calculations. We present illustrative applications of these approaches and discuss challenges and future perspectives for the field.SCOPE OF REVIEWHybrid QM/MM approaches have rapidly become one of the most popular computational tools for studying chemical reactivity in biomolecular systems. However, the high cost involved in performing high-level QM calculations has limited the applicability of these approaches when calculating free energies of chemical processes. In this review, we present some of the advances in using reference potentials and mean field approximations to accelerate high-level QM/MM calculations. We present illustrative applications of these approaches and discuss challenges and future perspectives for the field.The use of physically-based simplifications has shown to effectively reduce the cost of high-level QM/MM calculations. In particular, lower-level reference potentials enable one to reduce the cost of expensive free energy calculations, thus expanding the scope of problems that can be addressed.MAJOR CONCLUSIONSThe use of physically-based simplifications has shown to effectively reduce the cost of high-level QM/MM calculations. In particular, lower-level reference potentials enable one to reduce the cost of expensive free energy calculations, thus expanding the scope of problems that can be addressed.As was already demonstrated 40 years ago, the usage of simplified models still allows one to obtain cutting edge results with substantially reduced computational cost. This article is part of a Special Issue entitled Recent developments of molecular dynamics.GENERAL SIGNIFICANCEAs was already demonstrated 40 years ago, the usage of simplified models still allows one to obtain cutting edge results with substantially reduced computational cost. This article is part of a Special Issue entitled Recent developments of molecular dynamics. times We present some of the advances to accelerate high-level QM/MM calculations. Recent years have seen enormous progress in the development of methods for modeling (bio)molecular systems. This has allowed for the simulation of ever larger and more complex systems. However, as such complexity increases, the requirements needed for these models to be accurate and physically meaningful become more and more difficult to fulfill. The use of simplified models to describe complex biological systems has long been shown to be an effective way to overcome some of the limitations associated with this computational cost in a rational way. Hybrid QM/MM approaches have rapidly become one of the most popular computational tools for studying chemical reactivity in biomolecular systems. However, the high cost involved in performing high-level QM calculations has limited the applicability of these approaches when calculating free energies of chemical processes. In this review, we present some of the advances in using reference potentials and mean field approximations to accelerate high-level QM/MM calculations. We present illustrative applications of these approaches and discuss challenges and future perspectives for the field. The use of physically-based simplifications has shown to effectively reduce the cost of high-level QM/MM calculations. In particular, lower-level reference potentials enable one to reduce the cost of expensive free energy calculations, thus expanding the scope of problems that can be addressed. As was already demonstrated 40 years ago, the usage of simplified models still allows one to obtain cutting edge results with substantially reduced computational cost. This article is part of a Special Issue entitled Recent developments of molecular dynamics. |
| Author | Amrein, Beat A. Kamerlin, Shina C.L. Duarte, Fernanda Blaha-Nelson, David |
| AuthorAffiliation | Science for Life Laboratory, Department of Cell and Molecular Biology (ICM), Uppsala University, BMC Box 596, S-751 24 Uppsala, Sweden |
| AuthorAffiliation_xml | – name: Science for Life Laboratory, Department of Cell and Molecular Biology (ICM), Uppsala University, BMC Box 596, S-751 24 Uppsala, Sweden |
| Author_xml | – sequence: 1 givenname: Fernanda surname: Duarte fullname: Duarte, Fernanda email: fernanda.duarte@icm.uu.se – sequence: 2 givenname: Beat A. surname: Amrein fullname: Amrein, Beat A. – sequence: 3 givenname: David surname: Blaha-Nelson fullname: Blaha-Nelson, David – sequence: 4 givenname: Shina C.L. surname: Kamerlin fullname: Kamerlin, Shina C.L. email: kamerlin@icm.uu.se |
| BackLink | https://www.ncbi.nlm.nih.gov/pubmed/25038480$$D View this record in MEDLINE/PubMed https://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-251670$$DView record from Swedish Publication Index |
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| Snippet | Recent years have seen enormous progress in the development of methods for modeling (bio)molecular systems. This has allowed for the simulation of ever larger... times We present some of the advances to accelerate high-level QM/MM calculations. • We present some of the advances to accelerate high-level QM/MM calculations. • Quantitative limitations of low-level methods can be overcome by these... Background: Recent years have seen enormous progress in the development of methods for modeling (bio)molecular systems. This has allowed for the simulation of... |
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| SubjectTerms | Averaging potential Chlorides - chemistry cost effectiveness Energy Transfer Ethylene Dichlorides - chemistry Gibbs free energy Hydrolases - chemistry Kinetics Mean field approximation Methyl Chloride - chemistry molecular dynamics Molecular Dynamics Simulation - standards Multiscale modeling Protein Conformation Protein Folding Protein Stability Protein Unfolding Proteins - chemistry QM/MM free energy calculation Reference potential Reference Standards Review Structure-Activity Relationship Surface Properties Thermodynamics Uracil - chemistry |
| Title | Recent advances in QM/MM free energy calculations using reference potentials |
| URI | https://dx.doi.org/10.1016/j.bbagen.2014.07.008 https://www.ncbi.nlm.nih.gov/pubmed/25038480 https://www.proquest.com/docview/1700682599 https://www.proquest.com/docview/1823950221 https://www.proquest.com/docview/2000229493 https://pubmed.ncbi.nlm.nih.gov/PMC4547088 https://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-251670 |
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