Related papers: Polarisable force fields: What do they add in biom…
In this perspective, we discuss where and how accounting for electronic many-body polarization affects the accuracy of classical molecular dynamics simulations of biomolecules.While the effects of electronic polarization are highly…
The inclusion of electronic polarization is of crucial importance in molecular simulations of systems containing charged moieties. When neglected, as often done in force field simulations, charge-charge interactions in solution may become…
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…
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,…
Machine learning force fields offer the ability to simulate biomolecules with quantum mechanical accuracy while significantly reducing computational costs, attracting growing attention in biophysics. Meanwhile, leveraging the efficiency 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…
Extensions and improvements of empirical force fields are discussed in view of applications to computational vibrational spectroscopy and reactive molecular dynamics simulations. Particular focus is on quantitative studies which make…
Although a great number of computational models of water are available today, the majority of current biological simulations are done with simple models, such as TIP3P and SPC, developed almost thirty years ago and only slightly modified…
The biomolecules in and around a living cell -- proteins, nucleic acids, lipids, carbohydrates -- continuously sample myriad conformational states that are thermally accessible at physiological temperatures. Simultaneously, a given…
Microscopic stress fields are widely used in molecular simulations to understand mechanical behavior. Recently, decomposition methods of multibody forces to central force pairs between the interacting particles have been proposed. Here, we…
Molecular dynamics simulations of biomolecules have been widely adopted in biomedical studies. As classical point-charge models continue to be used in routine biomolecular applications, there have been growing demands on developing…
Distributed point charge models (DCM) and their minimal variants (MDCM) have been integrated with tools widely used for condensed-phase simulations, including a virial-based barostat and a slow-growth algorithm for thermodynamic…
Molecular dynamics (MD) simulations employing classical force fields constitute the cornerstone of contemporary atomistic modeling in chemistry, biology, and materials science. However, the predictive power of these simulations is only as…
Accurate modelling of electrostatic interactions and charge transfer is fundamental to computational chemistry, yet most machine learning interatomic potentials (MLIPs) rely on local atomic descriptors that cannot capture long-range…
This paper deals with the complex problem of how to simulate multiparticle contacts. The collision process is responsible for the transfer and dissipation of energy in granular media. A novel model of the interaction force between particles…
Quantum Mechanics/Molecular Mechanics (QM/MM) simulations are a popular approach to study various features of large systems. A common application of QM/MM calculations is in the investigation of reaction mechanisms in condensed-phase and…
Much of our mechanistic understanding of the functions of biological macromolecules is based on static structural experiments, which can be modelled either as single structures or conformational ensembles. While these provide us with…
Long ranged electrostatic interactions are time consuming to calculate in molecular dynamics and Monte-Carlo simulations. We introduce an algorithmic framework for simulating charged particles which modifies the dynamics so as to allow…
Our understanding of the physics of biological molecules, such as proteins and DNA, is limited because the approximations we usually apply to model inert materials are not in general applicable to soft, chemically inhomogeneous systems. The…
Molecular simulations and biophysical experiments can be used to provide independent and complementary insights into the molecular origin of biological processes. A particularly useful strategy is to use molecular simulations as a modelling…