Related papers: Perspective: Non-conventional Force Fields for App…
Biomolecular force fields have been traditionally derived based on a mixture of reference quantum chemistry data and experimental information obtained on small fragments. However, the possibility to run extensive molecular dynamics…
An overview of computational methods to describe high-dimensional potential energy surfaces suitable for atomistic simulations is given. Particular emphasis is put on accuracy, computability, transferability and extensibility of the methods…
Reactive force fields for molecular dynamics have enabled a wide range of studies in numerous material classes. These force fields are computationally inexpensive as compared to electronic structure calculations and allow for simulations of…
Vibrational spectroscopy is a powerful technique to characterize the near-equilibrium dynamics of molecules in the gas- and the condensed-phase. This contribution summarizes efforts from computer-based methods to gain insight into the…
Machine learning encompasses a set of tools and algorithms which are now becoming popular in almost all scientific and technological fields. This is true for molecular dynamics as well, where machine learning offers promises of extracting…
The concept of molecular mechanics force field has been widely accepted nowadays for studying various processes in biomolecular systems. In this paper, we suggest a modification for the standard CHARMM force field that permits simulations…
The quality of biomolecular simulations critically depends on the accuracy of the force field used to calculate the potential energy of the molecular configurations. Currently, most simulations employ non-polarisable force fields, which…
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…
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…
Physically-inspired latent force models offer an interpretable alternative to purely data driven tools for inference in dynamical systems. They carry the structure of differential equations and the flexibility of Gaussian processes,…
Biomolecular thermodynamics and spectroscopy depend on relative conformer energies, local curvatures, and collective dipole fluctuations on the potential-energy surface. Conventional molecular mechanics force fields enable large-scale…
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…
Radioactive molecules provide a powerful new platform in the search for new physics at energy scales complementary to high-energy particle colliders. By combining enhancements from nuclear properties with the sensitivity and control offered…
Force fields developed with machine learning methods in tandem with quantum mechanics are beginning to find merit, given their (i) low cost, (ii) accuracy, and (iii) versatility. Recently, we proposed one such approach, wherein, the…
The development of reliable and extensible molecular mechanics (MM) force fields -- fast, empirical models characterizing the potential energy surface of molecular systems -- is indispensable for biomolecular simulation and computer-aided…
We discuss semiempirical approaches and parametric methods developed for modeling molecular vibronic spectra. These methods, together with databases of molecular fragments, have proved efficient and flexible for solving various problems…
This review article provides an overview of structurally oriented experimental datasets that can be used to benchmark protein force fields, focusing on data generated by nuclear magnetic resonance (NMR) spectroscopy and room temperature…
The driving of vibrational motion by external electric fields is a topic of continued interest, due to the possibility of assessing new or metastable material phases with desirable properties. Here, we combine ab initio molecular dynamics…
Quantum mechanical methods have been devised for the elucidation and clarification of reaction paths of chemical processes over decades. While they are typically deployed in routine calculations on systems for which some insights have…
Coarse-grained (CG) molecular dynamics enables the study of biological processes at temporal and spatial scales that would be intractable at an atomistic resolution. However, accurately learning a CG force field remains a challenge. In this…