Wolf<sub>2</sub>Pack – Portal Based Atomistic Force-Field Development

Krämer-Fuhrmann, Ottmar; Neisius, Jens; Gehlen, Niklas; Reith, Dirk

doi:10.1021/ci300290g

Cited by 10 publications

(7 citation statements)

References 41 publications

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“…Here also, the approaches are too diverse to be listed exhaustively. They include in particular setup/simulation/analysis workflows, ,− as well as experimental databases and data-extraction procedures. − …”

Section: Introductionmentioning

confidence: 99%

Systematic Optimization of a Fragment-Based Force Field against Experimental Pure-Liquid Properties Considering Large Compound Families: Application to Saturated Haloalkanes

Oliveira

Andrey

Rieder

et al. 2020

J. Chem. Theory Comput.

100

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Direct optimization against experimental condensedphase properties concerning small organic molecules still represents the most reliable way to calibrate the empirical parameters of a force field. However, compared to a corresponding calibration against quantum-mechanical (QM) calculations concerning isolated molecules, this approach is typically very tedious and time-consuming. The present article describes an integrated scheme for the automated refinement of force-field parameters against experimental condensedphase data, considering entire classes of organic molecules constructed using a fragment library via combinatorial isomer enumeration. The main steps of the scheme, referred to as CombiFF, are as follows: (i) definition of a molecule family; (ii) combinatorial enumeration of all isomers; (iii) query for experimental data; (iv) automatic construction of the molecular topologies by fragment assembly; and (v) iterative refinement of the force-field parameters considering the entire family. As a first application, CombiFF is used here to design a GROMOS-compatible united-atom force field for the saturated acyclic haloalkane family. This force field relies on an electronegativity-equalization scheme for the atomic partial charges and involves no specific terms for σ-holes and halogen bonding. A total of 749 experimental liquid densities ρ liq and vaporization enthalpies ΔH vap concerning 486 haloalkanes are considered for calibration and validation. The resulting root-mean-square deviations from experiment are 49.8 (27.6) kg•m −3 for ρ liq and 2.7 (1.8) kJ•mol −1 for ΔH vap for the calibration (validation) set. The values are lower for the validation set which contains larger molecules (stronger influence of purely aliphatic interactions). The trends in the optimized parameters along the halogen series and across the compound family are in line with chemical intuition based on considerations related to size, polarizability, softness, electronegativity, induction, and hyperconjugation. This observation is particularly remarkable considering that the force-field calibration did not involve any QM calculation. Once the time-consuming task of target-data selection/curation has been performed, the optimization of a force field only takes a few days. As a result, CombiFF enables an easy assessment of the consequences of functional-form decisions on the accuracy of a force field at an optimal level of parametrization.

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Section: Introductionmentioning

confidence: 99%

Systematic Optimization of a Fragment-Based Force Field against Experimental Pure-Liquid Properties Considering Large Compound Families: Application to Saturated Haloalkanes

Oliveira

Andrey

Rieder

et al. 2020

J. Chem. Theory Comput.

100

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“…The Lennard-Jones parameters of phosgene, x = (σ C , σ O , σ Cl , ε C , ε O , ε Cl ), were optimized in order to reproduce the saturated liquid density ρ l at temperatures ranging from 235 K to 280 K. The molecular model includes fixed bond lengths and angles, an improper dihedral, four partial point charges at the atom centers, and Lennard-JonesParameters for three atom types [22]. The intermolecular parameters and partial atomic charges were derived from quantum mechanical calculations using GAMESS and WOLF 2 PACK, respectively [52][53][54]. Parallel N pT simulations were carried out at vapor liquid equilibrium for seven temperatures and their corresponding pressures, using GROMACS [55].…”

Section: Definiton Of the Simulation Systemsmentioning

confidence: 99%

Automated parameterization of intermolecular pair potentials using global optimization techniques

Krämer

Hülsmann

Köddermann

et al. 2014

Computer Physics Communications

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In this work, different global optimization techniques are assessed for the automated development of molecular force fields, as used in molecular dynamics and Monte Carlo simulations. The quest of finding suitable force field parameters is treated as a mathematical minimization problem. Intricate problem characteristics such as extremely costly and even abortive simulations, noisy simulation results, and especially multiple local minima naturally lead to the use of sophisticated global optimization algorithms. Five diverse algorithms (pure random search, recursive random search, CMA-ES, differential evolution, and taboo search) are compared to our own tailor-made solution named CoSMoS. CoSMoS is an automated workflow. It models the parameters' influence on the simulation observables to detect a globally optimal set of parameters. It is shown how and why this approach is superior to other algorithms. Applied to suitable test functions and simulations for phosgene, CoSMoS effectively reduces the number of required simulations and real time for the optimization task.

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“…Quantum mechanical calculations of partial atomic charges were realized, e.g., by [9]. In related work [10,11], the automized optimization workflow, WOLF 2 PACK, was created, which combines quantum mechanical algorithms with atomistic models and is capable of calculating both optimal intramolecular force field parameters and partial atomic charges. For the intermolecular part of Equation (1), the respective force field parameters were mostly adjusted to experimental target data, i.e., physical properties resulting from a molecular simulation were compared with experimental reference data.…”

Section: Force Field Parameterizationmentioning

confidence: 99%

“…As the combination technique is used, the grid points of the sparse grid are determined hierarchically from the required subgrids, cf. Equation (11). Let y ,j be a point of the subgrids of the level, = ( 1 , ..., N ), and position, j = (j 1 , ..., j N ), which is, at the same time, a non-boundary point of the sparse grid.…”

Section: Structurementioning

confidence: 99%

SpaGrOW—A Derivative-Free Optimization Scheme for Intermolecular Force Field Parameters Based on Sparse Grid Methods

Hülsmann

Reith

2013

Entropy

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Molecular modeling is an important subdomain in the field of computational modeling, regarding both scientific and industrial applications. This is because computer simulations on a molecular level are a virtuous instrument to study the impact of microscopic on macroscopic phenomena. Accurate molecular models are indispensable for such simulations in order to predict physical target observables, like density, pressure, diffusion coefficients or energetic properties, quantitatively over a wide range of temperatures. Thereby, molecular interactions are described mathematically by force fields. The mathematical description includes parameters for both intramolecular and intermolecular interactions.While intramolecular force field parameters can be determined by quantum mechanics, the parameterization of the intermolecular part is often tedious. Recently, an empirical procedure, based on the minimization of a loss function between simulated and experimental physical properties, was published by the authors. Thereby, efficient gradient-based numerical optimization algorithms were used. However, empirical force field optimization is inhibited by the two following central issues appearing in molecular simulations: firstly, they are extremely time-consuming, even on modern and high-performance computer clusters, and secondly, simulation data is affected by statistical noise. The latter provokes the fact that an accurate computation of gradients or Hessians is nearly impossible close to a local or global minimum, mainly because the loss function is flat. Therefore, the question arises of whether to apply a derivative-free method approximating Entropy 2013, 15 3641 the loss function by an appropriate model function. In this paper, a new Sparse Grid-based Optimization Workflow (SpaGrOW) is presented, which accomplishes this task robustly and, at the same time, keeps the number of time-consuming simulations relatively small. This is achieved by an efficient sampling procedure for the approximation based on sparse grids, which is described in full detail: in order to counteract the fact that sparse grids are fully occupied on their boundaries, a mathematical transformation is applied to generate homogeneous Dirichlet boundary conditions. As the main drawback of sparse grids methods is the assumption that the function to be modeled exhibits certain smoothness properties, it has to be approximated by smooth functions first. Radial basis functions turned out to be very suitable to solve this task. The smoothing procedure and the subsequent interpolation on sparse grids are performed within sufficiently large compact trust regions of the parameter space. It is shown and explained how the combination of the three ingredients leads to a new efficient derivative-free algorithm, which has the additional advantage that it is capable of reducing the overall number of simulations by a factor of about two in comparison to gradient-based optimization methods. At the same time, the robustness with respect to statistical noise is...

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Wolf₂Pack – Portal Based Atomistic Force-Field Development

Cited by 10 publications

References 41 publications

Systematic Optimization of a Fragment-Based Force Field against Experimental Pure-Liquid Properties Considering Large Compound Families: Application to Saturated Haloalkanes

Systematic Optimization of a Fragment-Based Force Field against Experimental Pure-Liquid Properties Considering Large Compound Families: Application to Saturated Haloalkanes

Automated parameterization of intermolecular pair potentials using global optimization techniques

SpaGrOW—A Derivative-Free Optimization Scheme for Intermolecular Force Field Parameters Based on Sparse Grid Methods

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Wolf2Pack – Portal Based Atomistic Force-Field Development

Cited by 10 publications

References 41 publications

Systematic Optimization of a Fragment-Based Force Field against Experimental Pure-Liquid Properties Considering Large Compound Families: Application to Saturated Haloalkanes

Systematic Optimization of a Fragment-Based Force Field against Experimental Pure-Liquid Properties Considering Large Compound Families: Application to Saturated Haloalkanes

Automated parameterization of intermolecular pair potentials using global optimization techniques

SpaGrOW—A Derivative-Free Optimization Scheme for Intermolecular Force Field Parameters Based on Sparse Grid Methods

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Wolf₂Pack – Portal Based Atomistic Force-Field Development