Where Lennard-Jones Potentials Fail: Iterative Optimization of Ion–Water Pair Potentials Based on Ab Initio Molecular Dynamics Data

Bernhardt, Marvin P.; Nagata, Yuki; Vegt, Nico F. A. van der

doi:10.1021/acs.jpclett.2c00121

Cited by 17 publications

(24 citation statements)

References 51 publications

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“…We have in the past used IMC and IBI alternately to get rid of those artifacts when a single IBI prerun has not worked. 33 With our improvement to the IMC matrix, the IMC method can be used directly in most cases without any prerun.…”

Section: Theorymentioning

confidence: 99%

“…In previous studies, IBI was often used before IMC, which makes sense due to IBI’s good convergence behavior at the onset region. We have in the past used IMC and IBI alternately to get rid of those artifacts when a single IBI prerun has not worked . With our improvement to the IMC matrix, the IMC method can be used directly in most cases without any prerun.…”

Section: Theorymentioning

confidence: 99%

See 1 more Smart Citation

Stability, Speed, and Constraints for Structural Coarse-Graining in VOTCA

Bernhardt

Hanke

Vegt

2023

J. Chem. Theory Comput.

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Structural coarse-graining involves the inverse problem of deriving pair potentials that reproduce target radial distribution functions. Despite its clear mathematical formulation, there are open questions about the existing methods concerning speed, stability, and physical representability of the resulting potentials. In this work, we make progress on several aspects of iterative methods used to solve the inverse problem. Based on integral equation theory, we derive fast Gauss−Newton schemes applicable to very general systems, including molecules with bonds and mixtures. Our methods are similar to inverse Monte Carlo in terms of convergence speed and have a similar cost per iteration as iterative Boltzmann inversion. We investigate stability problems in our schemes and in the inverse Monte Carlo method and propose modifications to fix them. Furthermore, we establish how the pair potential can be constrained at each iteration to reproduce the pressure, Kirkwood−Buff integral, or the enthalpy of vaporization. We demonstrate the potential of our approach in deriving coarsegrained force fields for nine different solvents and their mixtures. All methods described are implemented in the free and open VOTCA software framework for systematic coarse-graining.

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Section: Theorymentioning

confidence: 99%

Section: Theorymentioning

confidence: 99%

Stability, Speed, and Constraints for Structural Coarse-Graining in VOTCA

Bernhardt

Hanke

Vegt

2023

J. Chem. Theory Comput.

Self Cite

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“…Rather, he argues that more physics needs to be introduced in FFs . For example, it has been known for a long time that the description of the repulsive part of the Lennard-Jones potential , is not very accurate and variations of the Buckingham potential are to be preferred. − …”

Section: Introductionmentioning

confidence: 99%

An Imbalance in the Force: The Need for Standardized Benchmarks for Molecular Simulation

Kříž

Schmidt

Andersson

et al. 2023

J. Chem. Inf. Model.

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Force fields (FFs) for molecular simulation have been under development for more than half a century. As with any predictive model, rigorous testing and comparisons of models critically depends on the availability of standardized data sets and benchmarks. While such benchmarks are rather common in the fields of quantum chemistry, this is not the case for empirical FFs. That is, few benchmarks are reused to evaluate FFs, and development teams rather use their own training and test sets. Here we present an overview of currently available tests and benchmarks for computational chemistry, focusing on organic compounds, including halogens and common ions, as FFs for these are the most common ones. We argue that many of the benchmark data sets from quantum chemistry can in fact be reused for evaluating FFs, but new gas phase data is still needed for compounds containing phosphorus and sulfur in different valence states. In addition, more nonequilibrium interaction energies and forces, as well as molecular properties such as electrostatic potentials around compounds, would be beneficial. For the condensed phases there is a large body of experimental data available, and tools to utilize these data in an automated fashion are under development. If FF developers, as well as researchers in artificial intelligence, would adopt a number of these data sets, it would become easier to compare the relative strengths and weaknesses of different models and to, eventually, restore the balance in the force.

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“…4 For example, it has been known for a long time that the description of the repulsive part of the Lennard-Jones potential 5,6 is not very accurate and variations of the Buckingham potential 7 should be used instead. [8][9][10][11] Another important issue in this respect is the addition of explicit polarization, reviewed by Jing et al 12 as well as other approaches to improve the description of electrostatics 4,13 or dispersion interactions. [14][15][16] In fact, it has been shown by several authors that the explicit inclusion of many-body interactions in the potential function improves the accuracy of a FF for predicting physico-chemical properties for different phases to unprecedented levels.…”

Section: Introductionmentioning

confidence: 99%

An Imbalance in the Force: The Need for Standardised Benchmarks for Molecular Simulation

Kříž

Schmidt

Andersson

et al. 2022

Preprint

View full text Add to dashboard Cite

Force fields (FF) for molecular simulation have been under development for more than half a century. As with any predictive model, rigorous testing and comparisons of models critically depends on the availability of standardized datasets and benchmarks. While such benchmarks are rather common in the fields of quantum chemistry, this is not the case for empirical FFs. That is, few benchmarks are re-used to evaluate FFs and development teams rather use their own test sets. Here we present an overview of currently available tests and benchmarks for computational chemistry, focusing on organic compounds, including halogens and common ions, as FFs for these are the most common ones. We argue that many of the benchmark datasets from quantum chemistry can in fact be re-used for evaluating FFs, but new gas phase data is still needed for compounds containing phosphor and sulfur. In addition, more non- equilibrium energies and forces are needed for compounds with halogens, P and S. For the condensed phases there is a large body of experimental data available and tools to utilise these data in an automated fashion are under development. If FF developers, as well as researchers in artificial intelligence would adopt a number of these datasets it would become easier to compare the relative strengths and weaknesses of different models and to, eventually, restore the balance in the force.

show abstract

Where Lennard-Jones Potentials Fail: Iterative Optimization of Ion–Water Pair Potentials Based on Ab Initio Molecular Dynamics Data

Cited by 17 publications

References 51 publications

Stability, Speed, and Constraints for Structural Coarse-Graining in VOTCA

Stability, Speed, and Constraints for Structural Coarse-Graining in VOTCA

An Imbalance in the Force: The Need for Standardized Benchmarks for Molecular Simulation

An Imbalance in the Force: The Need for Standardised Benchmarks for Molecular Simulation

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