Related papers: System-specific parameter optimization for non-pol…
Classical molecular dynamics (MD) simulations enable modeling of materials and examination of microscopic details that are not accessible experimentally. The predictive capability of MD relies on the force field (FF) used to describe…
Electronic structure methods offer in principle accurate predictions of molecular properties, however, their applicability is limited by computational costs. Empirical methods are cheaper, but come with inherent approximations and are…
Parameterization of interatomic forcefields is a necessary first step in performing molecular dynamics simulations. This is a non-trivial global optimization problem involving quantification of multiple empirical variables against one or…
We present a polarizable embedding quantum mechanics/molecular mechanics (QM/MM) framework for ground- and excited-state Complete Active Space Self-Consistent Field (CASSCF) calculations on molecules within complex environments, such as…
In this Chapter we review our works on force fields for molecular simulations of protein systems. We first discuss the functional forms of the force fields and present some extensions of the conventional ones. We then present various…
Molecular dynamics (MD) simulations are essential tools for unraveling atomistic insights into the structure and dynamics of condensed-phase systems. However, the universal and accurate prediction of macroscopic properties from ab initio…
Fast and accurate molecular force field (FF) parameterization is still an unsolved problem. Accurate FFs are not generally available for all molecules, like novel druglike molecules. While methods based on quantum mechanics (QM) exist to…
Simulations with an explicit description of intermolecular forces using electronic structure methods are still not feasible for many systems of interest. As a result, empirical methods such as force fields (FF) have become an established…
An implementation of the fast multiple method (FMM) is performed for magnetic systems with long-ranged dipolar interactions. Expansion in spherical harmonics of the original FMM is replaced by expansion of polynomials in Cartesian…
We propose a novel method for refining force-field parameters of protein systems. In this method, the agreement of the secondary-structure stability and instability between the protein conformations obtained by experiments and those…
Accurate force fields are necessary for predictive molecular simulations. However, developing force fields that accurately reproduce experimental properties is challenging. Here, we present a machine learning directed, multiobjective…
Polarizable force fields are gradually becoming a common choice for ionic soft matter, in particular for molecular dynamics (MD) simulations of ionic liquids (ILs) and deep eutectic solvents (DESs). The CL&Pol force field introduced in 2019…
Molecular dynamics simulations are an invaluable tool in numerous scientific fields. However, the ubiquitous classical force fields cannot describe reactive systems, and quantum molecular dynamics are too computationally demanding to treat…
The enormous structural and chemical diversity of metal-organic frameworks (MOFs) forces researchers to actively use simulation techniques on an equal footing with experiments. MOFs are widely known for outstanding adsorption properties, so…
Force matching is an established technique to generate effective potentials for molecular dynamics simulations from first-principles data. This method has been implemented in the open source code potfit. Here, we present a review of the…
The development of coarse-grained (CG) molecular models typically requires a time-consuming iterative tuning of parameters in order to have the approximated CG models behaving correctly and consistently with, e.g., available…
The calculation of caloric properties such as heat capacity, Joule-Thomson coefficients and the speed of sound by classical force-field-based molecular simulation methodology has received scant attention in the literature, particularly for…
Meshfree simulation methods are emerging as compelling alternatives to conventional mesh-based approaches, particularly in the fields of Computational Fluid Dynamics (CFD) and continuum mechanics. In this publication, we provide a…
The issues of electronic polarizability in molecular dynamics simulations are discussed. We argue that the charges of ionized groups in proteins, and charges of ions in conventional non-polarizable force fields such as CHARMM, AMBER,…
Hamiltonian simulation using product formulas is arguably the most straightforward and practical approach for algorithmic simulation of a quantum system's dynamics on a quantum computer. Here we present corrected product formulas (CPFs), a…