Effect Of Force Field Research Articles

Real Cost of Speed: The Effect of a Time-Saving Multiple-Time-Stepping Algorithm on the Accuracy of Molecular Dynamics Simulations.

To enhance efficiency in molecular dynamics simulations, forces that vary slowly are often evaluated less often than those that vary rapidly. We show that the multiple-time-step algorithm implemented in recent versions of GROMACS results in significant differences in the collective properties of a system under conditions where the system was previously stable. The implications of changing the simulation algorithm without assessment of potential artifacts on the parametrization and transferability of effective force fields are discussed.

Smoothing potential energy surface of proteins by hybrid coarse grained approach**Project supported by the National Basic Research Program of China (Grant No. 2013CB932803), the National Natural Science Foundation of China (Grant No. 11574310), and the Joint NSFC-ISF Research Program, jointly funded by the National Natural Science Foundation of China and the Israel Science Foundation (Grant No. 51561145002).

Coarse-grained (CG) simulations can more efficiently study large conformational changes of biological polymers but usually lose accuracies in the details. Lots of different hybrid models involving multiple different resolutions have been developed to overcome the difficulty. Here we propose a novel effective hybrid CG (hyCG) approach which mixes the fine-grained interaction and its average in CG space to form a more smoothing potential energy surface. The hyCG approximately reproduces the potential of mean force in the CG space, and multiple mixed potentials can be further combined together to form a single effective force field for achieving both high efficiency and high accuracy. We illustrate the hyCG method in Trp-cage and Villin headpiece proteins to exhibit the folding of proteins. The topology of the folding landscape and thus the folding paths are preserved, while the folding is boosted nearly one order of magnitude faster. It indicates that the hyCG approach could be applied as an efficient force field in proteins.

Direct folding simulation of helical proteins using an effective polarizable bond force field.

We report a direct folding study of seven helical proteins (, Trpcage, , C34, N36, , ) ranging from 17 to 53 amino acids through standard molecular dynamics simulations using a recently developed polarizable force field-Effective Polarizable Bond (EPB) method. The backbone RMSDs, radius of gyrations, native contacts and native helix content are in good agreement with the experimental results. Cluster analysis has also verified that these folded structures with the highest population are in good agreement with their corresponding native structures for these proteins. In addition, the free energy landscape of seven proteins in the two dimensional space comprised of RMSD and radius of gyration proved that these folded structures are indeed of the lowest energy conformations. However, when the corresponding simulations were performed using the standard (nonpolarizable) AMBER force fields, no stable folded structures were observed for these proteins. Comparison of the simulation results based on a polarizable EPB force field and a nonpolarizable AMBER force field clearly demonstrates the importance of polarization in the folding of stable helical structures.

Creating Atomic Models of Brittle Glasses for In Silico Mechanical Tests

Atomic level computer simulation has become indispensable in understanding the mechanical properties of glasses, among other properties. However, the majority of model glasses are more ductile than their intended experimental counterparts, partially reflected by the overestimation of the Poisson's ratio. We have previously introduced an effective force field tuning method of imposing an additional energy penalty term to embrittle a binary Lennard–Jones glass. Here, we improved this method by varying the applied range of the energy penalty. The new method stabilizes the model glass even for high energy penalty values. Furthermore, unlike the old method, there is no unintended reduction in density for brittle glasses. Uniaxial tension tests were conducted to show the ductile‐to‐brittle transition as the energy penalty increases in strength. Crack propagation simulation was also conducted to demonstrate the efficacy of studying brittle fracture using the model glass.

Understanding 2D atomic resolution imaging of the calcite surface in water by frequency modulation atomic force microscopy

Frequency modulation atomic force microscopy (FM-AFM) experiments were performed on the calcite (104) surface in pure water, and a detailed analysis was made of the 2D images at a variety of frequency setpoints. We observed eight different contrast patterns that reproducibly appeared in different experiments and with different measurement parameters. We then performed systematic free energy calculations of the same system using atomistic molecular dynamics to obtain an effective force field for the tip-surface interaction. By using this force field in a virtual AFM simulation we found that each experimental contrast could be reproduced in our simulations by changing the setpoint, regardless of the experimental parameters. This approach offers a generic method for understanding the wide variety of contrast patterns seen on the calcite surface in water, and is generally applicable to AFM imaging in liquids.

Atomistic modeling of flexoelectricity in periclase

Flexoelectricity is evolution of a macroscopic polarization due to a strain gradient. We present a molecular dynamics study of flexoelectricity in the cubic ionic MgO periclase phase. Using an effective interaction force field with polarizable oxygen atoms and applying it to an inhomogeneously strained periclase sample, we detect a collective flexoelectric response of the oxygen dipole moments in visualizations. This induced polarization depends linearly on the strength of the strain gradient as well as the primary polarization, which is caused by the displacement of the ion charges. By three different inhomogeneous deformation modes all three flexoelectric coefficients of periclase are determined.

Adsorbed water on iron surface by molecular dynamics

The adsorption of H2O molecules on metal surfaces is important to understand the early process of water corrosion. This process can be described by computational simulation using molecular dynamics and Monte Carlo. However, this simulation demands an efficient description of the surface interactions between the water molecule and the metallic surface. In this study, an effective force field to describe the iron-water surface interactions was developed and it was used in a molecular dynamics simulation. The results showed a very good agreement between the simulated vibrational-DOS spectrum and the experimental vibrational spectrum of the iron–water interface. The water density profile revealed the presence of a water double layer in the metal interface. Furthermore, the horizontal mapping combined with the angular distribution of the molecular plane allowed the analysis of the water structure above the surface, which in turn agrees with the model of the double layer on metal surfaces.

Rigorous force field optimization principles based on statistical distance minimization.

We use the concept of statistical distance to define a measure of distinguishability between a pair of statistical mechanical systems, i.e., a model and its target, and show that its minimization leads to general convergence of the model's static measurable properties to those of the target. We exploit this feature to define a rigorous basis for the development of accurate and robust effective molecular force fields that are inherently compatible with coarse-grained experimental data. The new model optimization principles and their efficient implementation are illustrated through selected examples, whose outcome demonstrates the higher robustness and predictive accuracy of the approach compared to other currently used methods, such as force matching and relative entropy minimization. We also discuss relations between the newly developed principles and established thermodynamic concepts, which include the Gibbs-Bogoliubov inequality and the thermodynamic length.

Molecular Dynamics Study for Lithium Ion Diffusion in Layered LixCoO2 (x=0.5~1.0)

Diffusion constant of lithium ion is one of the most important properties in cathode materials for lithium ion battery. Various experimental and theoretical approaches have been studied to investigate the diffusion constant in LiCoO2 [1-6]. Lithium vacancy ordering is essential phenomenon to determine the lithium ion dynamics [7, 8] and it is important to understand the relationship between the ordered phase generation and the diffusion constant. In theoretical approach, ab initio calculations using density functional theory (DFT) have been established to evaluate the lithium ion diffusivity in cathodes from lithium hopping model based on activation barrier [4-6]. However, DFT is not appropriate for large simulation including various vacancy configurations because of computational cost explosion. Alternatively, molecular dynamics (MD) is more suitable approach to simulate over ten thousand atoms and MD can directly simulate the lithium diffusion with effective force field. However, generic force field cannot support for variable lithium ion number in LiCoO2 [9-12], because the force field development is difficult under the drastic electronic state changing of cobalt by lithium ion extraction/injection processes. Here, we have improved the force field using embedded atom method to modify the total energies in accordance with amount of neighboring lithium ion. The force field parameters have been optimized to reproduce potential energy surfaces of several lithium diffusion paths estimated by DFT calculations. We also fit vacancy energies and elastic constants at several lithium configurations. In addition, ab initio MD results are used as a reference to reproduce finite temperature fluctuation. For validation, MD simulations in several temperatures were performed. The diffusion constants calculated from mean square displacement of lithium ion were good agreement with experimental results [1, 2] qualitatively. We will talk about microscopic picture of lithium vacancy ordering on that day.

Nuclear Quantum Effects in Water: A Multiscale Study.

We outline a method to investigate the role of nuclear quantum effects in liquid water making use of a force field derived from ab initio simulations. Starting from a first-principles molecular dynamics simulation, we obtain an effective force field for bulk liquid water using the force-matching technique. After validating that our effective model reproduces the key structural and dynamic properties of the reference system, we use it to perform path integral simulations to investigate the role played by nuclear quantum effects on bulk water, probing radial distribution functions, vibrational spectra, and hydrogen bond fluctuations. Our approach offers a practical route to derive ab initio quality molecular models to study quantum effects at a low computational cost.

Visualization and Analysis of Vortex-Turbine Intersections in Wind Farms

Characterizing the interplay between the vortices and forces acting on a wind turbine's blades in a qualitative and quantitative way holds the potential for significantly improving large wind turbine design. This paper introduces an integrated pipeline for highly effective wind and force field analysis and visualization. We extract vortices induced by a turbine's rotation in a wind field, and characterize vortices in conjunction with numerically simulated forces on the blade surfaces as these vortices strike another turbine's blades downstream. The scientifically relevant issue to be studied is the relationship between the extracted, approximate locations on the blades where vortices strike the blades and the forces that exist in those locations. This integrated approach is used to detect and analyze turbulent flow that causes local impact on the wind turbine blade structure. The results that we present are based on analyzing the wind and force field data sets generated by numerical simulations, and allow domain scientists to relate vortex-blade interactions with power output loss in turbines and turbine life expectancy. Our methods have the potential to improve turbine design to save costs related to turbine operation and maintenance.

Fracture model of brittle and quasibrittle materials and geomedia

A general model and a unified mathematical formalism are proposed for description of inelastic deformation and fracture of any solids, where brittle or plastic, as their evolution in effective force fields. Loaded solids and media are considered as nonlinear dynamic systems. One of the main tasks of the work is to show that if deformation and fracture of a strong medium is treated as its evolution in effective force fields, numerical solutions of equations of solid mechanics do demonstrate the fundamental properties of nonlinear dynamic systems—self-organized criticality and two-stage evolution (a rather slow quasistationary stage and a superfast catastrophic stage or a blowup mode). The model is tested by simulation of fracture of quasibrittle composites under axial compression. Calculations are also presented for the now developing tectonic flows and seismic processes in Central Asia, including the Baikal rift zone and the Altai-Sayany folded region. It is shown that numerical solutions of all examined problems of inelastic deformation and fracture demonstrate self-organized criticality of loaded media, including peculiarities of slow dynamics and spatial-temporal migration of deformation activity, and as well as two-stage fracture: comparatively slow quasi-equilibrium damage accumulation and superfast catastrophic fracture. The predicted seismic events obey the Gutenberg-Richter law.

SAFT-γ Force Field for the Simulation of Molecular Fluids: 2. Coarse-Grained Models of Greenhouse Gases, Refrigerants, and Long Alkanes

In the first paper of this series [C. Avendaño, T. Lafitte, A. Galindo, C. S. Adjiman, G. Jackson, and E. A. Müller, J. Phys. Chem. B2011, 115, 11154] we introduced the SAFT-γ force field for molecular simulation of fluids. In our approach, a molecular-based equation of state (EoS) is used to obtain coarse-grained (CG) intermolecular potentials that can then be employed in molecular simulation over a wide range of thermodynamic conditions of the fluid. The macroscopic experimental data for the vapor-liquid equilibria (saturated liquid density and vapor pressure) of a given system are represented with the SAFT-VR Mie EoS and used to estimate effective intermolecular parameters that provide a good description of the thermodynamic properties by exploring a wide parameter space for models based on the Mie (generalized Lennard-Jones) potential. This methodology was first used to develop a simple single-segment CG Mie model of carbon dioxide (CO2) which allows for a reliable representation of the fluid-phase equilibria (for which the model was parametrized), as well as an accurate prediction of other properties such as the enthalpy of vaporization, interfacial tension, supercritical density, and second-derivative thermodynamic properties (thermal expansivity, isothermal compressibility, heat capacity, Joule-Thomson coefficient, and speed of sound). In our current paper, the methodology is further applied and extended to develop effective SAFT-γ CG Mie force fields for some important greenhouse gases including carbon tetrafluoride (CF4) and sulfur hexafluoride (SF6), modeled as simple spherical molecules, and for long linear alkanes including n-decane (n-C10H22) and n-eicosane (n-C20H42), modeled as homonuclear chains of spherical Mie segments. We also apply the SAFT-γ methodology to obtain a CG homonuclear two-segment Mie intermolecular potential for the more challenging polar and asymmetric compound 2,3,3,3-tetrafluoro-1-propene (HFO-1234yf), a novel replacement refrigerant with promising properties. The description of the fluid-phase behavior and the prediction of the other thermophysical properties obtained by molecular simulation using our SAFT-γ CG Mie force fields are found to be of comparable quality (and sometimes superior) to that obtained using the more sophisticated all-atom (AA) and united-atom (UA) models commonly employed in the field. We should emphasize that though the focus of our current work is on simple homonuclear models, the SAFT-γ methodology is based on a group contribution methodology which is naturally suited to the development of more sophisticated heteronuclear models.

An effective force field for molecular dynamics simulations of dimethyl sulfone

A rigid five-site united atom model for dimethyl sulfone (DMSO2) compatible with the GROMOS force field is parametrized and tested. The parameters were optimized with respect to experimental quantities such as liquid density, heat of vaporization, shear viscosity and excess free energy. Good agreement with pure component properties is achieved except for the static dielectric permittivity which is calculated too low. Together with the SPC model for water the new DMSO2 model was used to study aqueous mixtures at low concentrations and compared to aqueous mixtures of DMSO. It is concluded that interaction parameters for sulfoxide oxygen are not directly transferable to sulfonyl oxygen.

Kalman Smoother Based Force Localization and Mapping Using Intravital Video Microscopy

Motility is an important property of immune system cells. It provides cells with the ability to perform their function not only at the right time but also at the right place. In this paper, we introduce the problem of modeling and estimating an effective force field directing cell movement by the analysis of intravital video microscopy. A computational approach is proposed for solving this problem without dealing with a parametrized spatial model of the field in order to avoid potential errors due to inaccurate spatial model assumptions. We consider the dynamics of cells similar to the dynamics of distributed agents typically used in the field of swarm robotics. The method utilizes a fixed-interval Kalman filter based smoother. Its application results in a map giving the intensity and direction of the effective force field. The results show that real-time video images are a source of data, enabling us to visualize intriguing spatiotemporal phenomena inside immune system organs. The proposed approach can fill the existing gap between contemporary technology and quantitative data analyses present in the field of biosystems.

Effective Fragment Molecular Orbital Method: A Merger of the Effective Fragment Potential and Fragment Molecular Orbital Methods†

We present a new method called the effective fragment molecular orbital (EFMO) method. The EFMO method is a hybrid between the fragment molecular orbital (FMO) electronic structure method ( Kitaura , K. ; Ikeo , E. ; Asada , T. ; Nakano , T. ; Uebayasi , M. Chem. Phys. Lett. 1999 , 313 , 701 - 706 ) and the effective fragment potential multipole-based polarizable force field ( Day , P. N. ; Jensen , J. H. ; Gordon , M. S. ; Webb , S. P. ; Stevens , W. J. ; Krauss , M. ; Garmer , D. ; Basch , H. ; Cohen , D. J. Chem. Phys. 1996 , 105 , 1968 - 1986 ). The EFMO method is based on the FMO molecular fragmentation scheme and the many-body energy expression but uses the EFP multipole-based energy expressions for long-range interactions and for evaluating the many-body polarization. The accuracy and performance of the EFMO method is compared to FMO and conventional electronic structure theory for water clusters. The difference in the EFMO energy compared to that of conventional Hartree-Fock theory is roughly 0.5 kcal/mol per hydrogen using the 6-31G(d) basis set but less than 0.1 kcal/mol using the 6-31+G(d) basis set. The EFMO method is roughly two times faster than the FMO2 method using Hartree-Fock and five times when computing Hartree-Fock energy and gradients; preliminary density functional theory results are also presented.

Topological structure of the inter-band phase difference soliton in two-band superconductivity

Two-component superconductivity based on the two-band superconductor has a functional topology such as an inter-band phase difference soliton (i-soliton) to realize topological electronics (topolonics). Many gauge field theories are applied to investigate the topology of two-band superconductivity. To ease experimental and electronics applications, these theories should be refined. Weinberg–Salam theory and SU(2) (two-dimensional special unitary symmetry) gauge field theory are proper starting points. An effective extra force field because of the crystal structure and inter-band Josephson interaction, rather than spontaneous symmetry breaking, simplifies the conventional gauge field theory.

Direct construction of mesoscopic models from microscopic simulations.

Starting from microscopic molecular-dynamics (MD) simulations of constrained Lennard-Jones (LJ) clusters (with constant radius of gyration R(g)), we construct two mesoscopic models [Langevin dynamics and dissipative particle dynamics (DPD)] by coarse graining the LJ clusters into single particles. Both static and dynamic properties of the coarse-grained models are investigated and compared with the MD results. The effective mean force field is computed as a function of the intercluster distance, and the corresponding potential scales linearly with the number of particles per cluster and the temperature. We verify that the mean force field can reproduce the equation of state of the atomistic systems within a wide density range but the radial distribution function only within the dilute and the semidilute regime. The friction force coefficients for both models are computed directly from the time-correlation function of the random force field of the microscopic system. For high density or a large cluster size the friction force is overestimated and the diffusivity underestimated due to the omission of many-body effects as a result of the assumed pairwise form of the coarse-grained force field. When the many-body effect is not as pronounced (e.g., smaller R(g) or semidilute system), the DPD model can reproduce the dynamic properties of the MD system.

Discussion on: “Robust Fault Detection Observer and Fault Estimation Filter Design for LTI Systems Based on GKYP Lemma”

For the calculation of thermophysical properties of fluids with molecular dynamics (MD) simulations, effective force fields (FFs) which are optimized against experimental vapor-liquid equilibria are often used. Examples for this FF category are TraPPE, OPLS, and AMBER. An alternative are simplified pair-specific, ab initio-based FFs (AI-FFs), which are derived from quantum-chemical calculations in the limit of zero-density in combination with the kinetic theory of gases, and, thus, feature a predictive character. In the present study, we show with the help of selected binary fluid mixtures that the predictive power of MD simulations in calculating Fick diffusion coefficients can be improved using simplified pair-specific AI-FFs based on corresponding FFs for the pure substances. To evaluate the performance of the new AI-FFs in comparison with the TraPPE FFs, binary mixtures consisting of methane, carbon dioxide, and propane were investigated from the superheated vapor to the gas state and supercritical region up to the compressed liquid state. For the determination of the Fick diffusion coefficient at pressures between (0.1 and 12) MPa, temperatures between (293 and 355) K, and mole fractions between 0.05 and 0.95, separate simulations for the analysis of the Maxwell–Stefan diffusion coefficient and the thermodynamic factor were performed considering system size effects. With the exception of the compressed liquid state and regions in vicinity of the two-phase boundary, where the TraPPE FFs are generally superior, the AI-FFs show improved predictions for the Fick diffusion coefficient with average expanded statistical uncertainties of 12%. This could be demonstrated by comparison of the simulation results with the theoretical ab initio calculations and the available experimental data, resulting in average absolute deviations of 7% and 13% for the AI-FFs and TraPPE FFs.

Structure of Large Nitrate−Water Clusters at Ambient Temperatures: Simulations with Effective Fragment Potentials and Force Fields with Implications for Atmospheric Chemistry

Structural properties of large NO(3)(-).(H(2)O)(n) (n = 15-500) clusters are studied by Monte Carlo simulations using effective fragment potentials (EFPs) and by classical molecular dynamics simulations using a polarizable empirical force field. The simulation results are analyzed with a focus on the description of hydrogen bonding and solvation in the clusters. In addition, a comparison between the electronic structure based EFP and the classical force field description of the 32 water cluster system is presented. The EFP simulations, which focused on the cases of n = 15 and 32, show an internal, fully solvated structure and a "surface adsorbed" structure for the 32 water cluster at 300 K, with the latter configuration being more probable. The internal solvated structure and the "surface adsorbed" structure differ considerably in their hydrogen bonding coordination numbers. The force field based simulations agree qualitatively with these results, and the local geometry of NO(3)(-) and solvation at the surface-adsorbed site in the force field simulations are similar to those predicted using EFPs. Differences and similarities between the description of hydrogen bonding of the anion in the two approaches are discussed. Extensive classical force field based simulations at 250 K predict that long time scale stability of "internal" NO(3)(-), which is characteristic of extended bulk aqueous interfaces, emerges only for n > 300. Ab initio Møller-Plesset perturbation theory is used to test the geometries of selected surface and interior anions for n = 32, and the results are compared to the EFP and MD simulations. Qualitatively, all approaches agree that surface structures are preferred over the interior structures for clusters of this size. The relatively large aqueous clusters of NO(3)(-) studied here are of comparable size to clusters that lead to new particle formation in air. Nitrate ions on the surface of such clusters may have significantly different photochemistry than the internal species. The possible implications of surface-adsorbed nitrate ions for atmospheric chemistry are discussed.