Related papers: A concise introduction to molecular dynamics simul…
Large parallel gains in the development of both computational resources as well as sampling methods have now made it possible to simulate dissociation events in ligand-protein complexes with all--atom resolution. Such encouraging progress,…
The optimal conversion of a continuous inter-particle potential to a discrete equivalent is considered here. Existing and novel algorithms are evaluated to determine the best technique for creating accurate discrete forms using the minimum…
Machine learning plays an important and growing role in molecular simulation. The newest version of the OpenMM molecular dynamics toolkit introduces new features to support the use of machine learning potentials. Arbitrary PyTorch models…
Molecular dynamics (MD) simulation based on Langevin equation has been widely used in the study of structural, thermal properties of matters in difference phases. Normally, the atomic dynamics are described by classical equations of motion…
This study examines the simulation of quantum algorithms on a classical computer. The program code implemented on a classical computer will be a straight connection between the mathematical formulation of quantum mechanics and computational…
Based on a novel concept of multiplicative multiscale decomposition, we have derived a multiscale micromorphic molecular dynamics (MMMD)to extent the (Andersen)-Parrinello-Rahman molecular dynamics to mesoscale and macroscale. The…
We describe a parallelised version of the MOLDY molecular dynamics program. This Fortran code is aimed at systems which may be described by short-range potentials and specifically those which may be addressed with the embedded atom method.…
The molecular simulations solve the equation of motion of molecular systems, making 3D shapes of molecules four-dimensional by adding the time coordinate. These methods have a great potential in drug discovery because they can realistically…
We derive a formulation of molecular dynamics that generates only symmetric configurations. We implement it for all 2D planar and 3D space groups. An atlas of 2D Lennard-Jones crystals under all planar groups is created with symmetric…
The interfaces between metal electrodes and liquid electrolytes are prototypical in electrochemistry. That is why it is crucial to have a molecular and dynamical understating of such interfaces for both electrical properties and chemical…
Conformational dynamics is crucial for ribonucleic acid (RNA) function. Techniques such as nuclear magnetic resonance, cryo-electron microscopy, small- and wide-angle X-ray scattering, chemical probing, single-molecule F\"orster resonance…
We report a new Quantum Mechanical/Molecular Dynamics (QM/MD) simulation loop to model the coupling between the electron and atom dynamics in solid/liquid interfacial systems. The method can describe simultaneously both the quantum…
The physical processes at the interface of a low-temperature plasma and a solid are extremely complex. They involve a huge number of elementary processes in the plasma, in the solid as well as charge, momentum and energy transfer across the…
Visual Molecular Dynamics (VMD) is one of the most widely used molecular graphics software in the community of theoretical simulations. So far, however, it still lacks a graphical user interface (GUI) for molecular manipulations when doing…
We present a continuum model trained on molecular dynamics (MD) simulations for cellular membranes composed of an arbitrary number of lipid types. The model is constructed within the formalism of dynamic density functional theory and can be…
Molecular dynamics (MD) simulations allow investigating the structural dynamics of biomolecular systems with unrivaled time and space resolution. However, in order to compensate for the inaccuracies of the utilized empirical force fields,…
In Molecular Dynamics (MD), the forces applied to atoms derive from potentials which describe the energy of bonds, valence angles, torsion angles, and Lennard-Jones interactions of which molecules are made. These de finitions are classic;…
The most interesting step of condensation is the cluster formation up to the critical size. In a closed system, this is an instationary process, as the vapour is depleted by the emerging liquid phase. This imposes a limitation on direct…
Machine learned interaction potentials (MLIPs) have become a critical component of large-scale, high-quality simulations for a range of chemical and biochemical systems. Yet, despite their in-distribution accuracy, molecular dynamics…
Molecular dynamics (MD) simulations play an important role in understanding and engineering heat transport properties of complex materials. An essential requirement for reliably predicting heat transport properties is the use of accurate…