相关论文: Automatic Parameterization of Force Fields for Liq…
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…
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…
Reactive molecular dynamics (MD) simulation is performed using a reactive force field (ReaxFF). To this end, we developed a new method to optimize the ReaxFF parameters based on a machine learning approach. This approach combines the…
Empirical force fields employed in molecular dynamics simulations of complex systems can be optimised to reproduce experimentally determined structural and thermodynamic properties. In contrast, experimental knowledge about the rates of…
Two of the most challenging tasks in molecular simulation consist in capturing the properties of systems with long-range interactions (e.g. electrolyte solutions) as well as systems containing large molecules such as hydrogels. For the…
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…
A parameterization strategy for molecular models on the basis of force fields is proposed, which allows a rapid development of models for small molecules by using results from quantum mechanical (QM) ab initio calculations and thermodynamic…
Exact characterization of phase transitions requires sufficient configurational sampling, necessitating efficient and accurate potential energy surfaces. Molecular force fields with computational efficiency and physical interpretability are…
In molecular dynamics (MD) simulation, force field determines the capability of an individual model in capturing physical and chemistry properties. The method for generating proper parameters of the force field form is the key component for…
Molecular simulations are essential tools in computational chemistry, enabling the prediction and understanding of molecular interactions and thermodynamic properties of biomolecules. However, traditional force fields face significant…
Theoretical studies on chemical reaction mechanisms have been crucial in organic chemistry. Traditionally, calculating the manually constructed molecular conformations of transition states for chemical reactions using quantum chemical…
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…
Developing accurate, transferable, and computationally-efficient interatomic forcefields is key to facilitate the modeling of silicate glasses. However, the high number of forcefield parameters that need to be optimized render traditional…
We develop coarse-grained force fields for poly (vinyl alcohol) and poly (acrylic acid) oligomers. In both cases, one monomer is mapped onto a coarse-grained bead. The new force fields are designed to match structural properties such as…
Hybrid particle-field methods are computationally efficient approaches for modelling soft matter systems. So far applications of these methodologies have been limited to constant volume conditions. Here, we reformulate particle-field…
The applicability of the three steps systematic parametrization procedure (3SSPP) to develop a force field for primary amines was evaluated in the present work. Previous simulations of primary amines show that current force fields (FF) can…
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…
We implemented a coarse-graining procedure to construct mesoscopic models of complex molecules. The final aim is to obtain better results on properties depending on slow modes of the molecules. Therefore the number of particles considered…
The hybrid particle-field molecular dynamics method is an efficient alternative to standard particle-based coarse grained approaches. In this work, we propose an automated protocol for optimisation of the effective parameters that define…
Metropolis simulations of all-atom models of peptides (i.e. small proteins) are considered. Inspired by the funnel picture of Bryngelson and Wolyness, a transformation of the updating probabilities of the dihedral angles is defined, which…