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Devereux M, Boittier ED, Meuwly M. Systematic improvement of empirical energy functions in the era of machine learning. J Comput Chem 2024; 45:1899-1913. [PMID: 38695412 DOI: 10.1002/jcc.27367] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 02/13/2024] [Accepted: 02/21/2024] [Indexed: 07/05/2024]
Abstract
The impact of targeted replacement of individual terms in empirical force fields is quantitatively assessed for pure water, dichloromethane (CH 2 Cl 2 ), and solvated K + and Cl - ions. For the electrostatic interactions, point charges (PCs) and machine learning (ML)-based minimally distributed charges (MDCM) fitted to the molecular electrostatic potential are evaluated together with electrostatics based on the Coulomb integral. The impact of explicitly including second-order terms is investigated by adding a fragment molecular orbital (FMO)-derived polarization energy to an existing force field, in this case CHARMM. It is demonstrated that anisotropic electrostatics reduce the RMSE for water (by 1.4 kcal/mol), CH 2 Cl 2 (by 0.8 kcal/mol) and for solvated Cl - clusters (by 0.4 kcal/mol). An additional polarization term can be neglected for CH 2 Cl 2 but further improves the models for pure water (by ∼ 1.0 kcal/mol) and hydrated Cl - (by 0.4 kcal/mol), and is key for solvated K + , reducing the RMSE by 2.3 kcal/mol. A 12-6 Lennard-Jones functional form performs satisfactorily with PC and MDCM electrostatics, but is not appropriate for descriptions that account for the electrostatic penetration energy. The importance of many-body contributions is assessed by comparing a strictly 2-body approach with self-consistent reference data. Two-body interactions suffice for CH 2 Cl 2 whereas water and solvated K + and Cl - ions require explicit many-body corrections. Finally, a many-body-corrected dimer potential energy surface exceeds the accuracy attained using a conventional empirical force field, potentially reaching that of an FMO calculation. The present work systematically quantifies which terms improve the performance of an existing force field and what reference data to use for parametrizing these terms in a tractable fashion for ML fitting of pure and heterogeneous systems.
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Affiliation(s)
- Mike Devereux
- Department of Chemistry, University of Basel, Basel, Switzerland
| | - Eric D Boittier
- Department of Chemistry, University of Basel, Basel, Switzerland
| | - Markus Meuwly
- Department of Chemistry, University of Basel, Basel, Switzerland
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2
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Wang L, Behara PK, Thompson MW, Gokey T, Wang Y, Wagner JR, Cole DJ, Gilson MK, Shirts MR, Mobley DL. The Open Force Field Initiative: Open Software and Open Science for Molecular Modeling. J Phys Chem B 2024; 128:7043-7067. [PMID: 38989715 DOI: 10.1021/acs.jpcb.4c01558] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/12/2024]
Abstract
Force fields are a key component of physics-based molecular modeling, describing the energies and forces in a molecular system as a function of the positions of the atoms and molecules involved. Here, we provide a review and scientific status report on the work of the Open Force Field (OpenFF) Initiative, which focuses on the science, infrastructure and data required to build the next generation of biomolecular force fields. We introduce the OpenFF Initiative and the related OpenFF Consortium, describe its approach to force field development and software, and discuss accomplishments to date as well as future plans. OpenFF releases both software and data under open and permissive licensing agreements to enable rapid application, validation, extension, and modification of its force fields and software tools. We discuss lessons learned to date in this new approach to force field development. We also highlight ways that other force field researchers can get involved, as well as some recent successes of outside researchers taking advantage of OpenFF tools and data.
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Affiliation(s)
- Lily Wang
- Open Force Field, Open Molecular Software Foundation, Davis, California 95616, United States
| | - Pavan Kumar Behara
- Center for Neurotherapeutics, University of California, Irvine, California 92697, United States
| | - Matthew W Thompson
- Open Force Field, Open Molecular Software Foundation, Davis, California 95616, United States
| | - Trevor Gokey
- Department of Chemistry, University of California, Irvine, California 92697, United States
| | - Yuanqing Wang
- Simons Center for Computational Physical Chemistry and Center for Data Science, New York, New York 10004, United States
| | - Jeffrey R Wagner
- Open Force Field, Open Molecular Software Foundation, Davis, California 95616, United States
| | - Daniel J Cole
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne NE1 7RU, United Kingdom
| | - Michael K Gilson
- Skaggs School of Pharmacy and Pharmaceutical Sciences, The University of California at San Diego, La Jolla, California 92093, United States
| | - Michael R Shirts
- Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, Colorado 80305, United States
| | - David L Mobley
- Department of Chemistry, University of California, Irvine, California 92697, United States
- Department of Pharmaceutical Sciences, University of California, Irvine, California 92697, United States
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Chung JK, Brown ML, Popelier PLA. Transferability of Buckingham Parameters for Short-Range Repulsion between Topological Atoms. J Phys Chem A 2024; 128:4561-4572. [PMID: 38805440 PMCID: PMC11163427 DOI: 10.1021/acs.jpca.4c02048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Revised: 05/16/2024] [Accepted: 05/20/2024] [Indexed: 05/30/2024]
Abstract
The repulsive part of the Buckingham potential, with parameters A and B, can be used to model deformation energies and steric energies. Both are calculated using the interacting quantum atom energy decomposition scheme where the latter is obtained from the former by a charge-transfer-based energy correction. These energies relate to short-range interactions, specifically the deformation of electron density and steric hindrance, respectively, when topological atoms approach each other. In this work, we calculate and fit the energies of carbonyl carbon, carbonyl oxygen, and, where possible, amine nitrogen atoms to the repulsive part of the Buckingham potential for 26 molecules. We find that while the steric energies of all atom pairs studied display exponential behavior with respect to distance, some deformation energy data do not. The obtained parameters are shown to be transferable by calculating root-mean-square errors of fitted potentials with respect to energy data of the same atom in, as far as possible, all other molecules from our data set. We observed that 36% and 10% of these errors were smaller than 4 kJ mol-1 for steric and deformation energy, respectively. Thus, we find that steric energy parameters are more transferable than deformation energy parameters. Finally, we speculate about the physical meaning of the A and B parameters and the implications of the strong exponential and exponential-linear piecewise relationships that we observe between them.
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Affiliation(s)
- Jaiming
J. K. Chung
- Department of Chemistry, The University of Manchester, Oxford Road, Manchester M13 9PL, Great
Britain
| | - Matthew L. Brown
- Department of Chemistry, The University of Manchester, Oxford Road, Manchester M13 9PL, Great
Britain
| | - Paul L. A. Popelier
- Department of Chemistry, The University of Manchester, Oxford Road, Manchester M13 9PL, Great
Britain
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4
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Wang L, Schauperl M, Mobley DL, Bayly C, Gilson MK. A Fast, Convenient, Polarizable Electrostatic Model for Molecular Dynamics. J Chem Theory Comput 2024; 20:1293-1305. [PMID: 38240687 PMCID: PMC10867846 DOI: 10.1021/acs.jctc.3c01171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2024]
Abstract
We present an efficient polarizable electrostatic model, utilizing typed, atom-centered polarizabilities and the fast direct approximation, designed for efficient use in molecular dynamics (MD) simulations. The model provides two convenient approaches for assigning partial charges in the context of atomic polarizabilities. One is a generalization of RESP, called RESP-dPol, and the other, AM1-BCC-dPol, is an adaptation of the widely used AM1-BCC method. Both are designed to accurately replicate gas-phase quantum mechanical electrostatic potentials. Benchmarks of this polarizable electrostatic model against gas-phase dipole moments, molecular polarizabilities, bulk liquid densities, and static dielectric constants of organic liquids show good agreement with the reference values. Of note, the model yields markedly more accurate dielectric constants of organic liquids, relative to a matched nonpolarizable force field. MD simulations with this method, which is currently parametrized for molecules containing elements C, N, O, and H, run only about 3.6-fold slower than fixed charge force fields, while simulations with the self-consistent mutual polarization average 4.5-fold slower. Our results suggest that RESP-dPol and AM1-BCC-dPol afford improved accuracy relative to fixed charge force fields and are good starting points for developing general, affordable, and transferable polarizable force fields. The software implementing these approaches has been designed to utilize the force field fitting frameworks developed and maintained by the Open Force Field Initiative, setting the stage for further exploration of this approach to polarizable force field development.
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Affiliation(s)
- Liangyue Wang
- Department
of Chemistry and Biochemistry, University
of California, San Diego, California 92093, United States
| | - Michael Schauperl
- HotSpot
Therapeutics, Inc., Boston, Massachusetts 02210, United States
| | - David L. Mobley
- Department
of Pharmaceutical Sciences, University of
California, Irvine, California 92697, United States
| | - Christopher Bayly
- OpenEye
Scientific, Cadence Molecular Sciences, Santa Fe, New Mexico 87508, United States
| | - Michael K. Gilson
- Skaggs
School of Pharmacy and Pharmaceutical Sciences, University of California, San
Diego, California 92093, United States
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Hosseini AN, van der Spoel D. Martini on the Rocks: Can a Coarse-Grained Force Field Model Crystals? J Phys Chem Lett 2024; 15:1079-1088. [PMID: 38261634 PMCID: PMC10839907 DOI: 10.1021/acs.jpclett.4c00012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Revised: 01/18/2024] [Accepted: 01/19/2024] [Indexed: 01/25/2024]
Abstract
Computational chemistry is an important tool in numerous scientific disciplines, including drug discovery and structural biology. Coarse-grained models offer simple representations of molecular systems that enable simulations of large-scale systems. Because there has been an increase in the adoption of such models for simulations of biomolecular systems, critical evaluation is warranted. Here, the stability of the amyloid peptide and organic crystals is evaluated using the Martini 3 coarse-grained force field. The crystals change shape drastically during the simulations. Radial distribution functions show that the distance between backbone beads in β-sheets increases by ∼1 Å, breaking the crystals. The melting points of organic compounds are much too low in the Martini force field. This suggests that Martini 3 lacks the specific interactions needed to accurately simulate peptides or organic crystals without imposing artificial restraints. The problems may be exacerbated by the use of the 12-6 potential, suggesting that a softer potential could improve this model for crystal simulations.
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Affiliation(s)
- A. Najla Hosseini
- Department of Cell and Molecular
Biology, Uppsala University, Box 596, SE-75124 Uppsala, Sweden
| | - David van der Spoel
- Department of Cell and Molecular
Biology, Uppsala University, Box 596, SE-75124 Uppsala, Sweden
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