Related papers: ESPResSo++ 2.0: Advanced methods for multiscale mo…

ESPResSo 4.0 is an extensible simulation package for research on soft matter. This versatile molecular dynamics program was originally developed for coarse-grained simulations of charged systems Limbach et al., Comput. Phys. Commun. 174,…

Molecular simulations are an important tool for research in physics, chemistry, and biology. The capabilities of simulations can be greatly expanded by providing access to advanced sampling methods and techniques that permit calculation of…

For the study of complex synthetic and biological molecular systems by computer simulations one is still restricted to simple model systems or to by far too small time scales. To overcome this problem multiscale techniques are being…

-Molecular simulations allow the study of properties and interactions of molecular systems. This article presents an improved version of the Adaptive Resolution Scheme that links two systems having atomistic (also called fine-grained) and…

MADNESS (multiresolution adaptive numerical environment for scientific simulation) is a high-level software environment for solving integral and differential equations in many dimensions that uses adaptive and fast harmonic analysis methods…

The Adaptive Poisson-Boltzmann Solver (APBS) software was developed to solve the equations of continuum electrostatics for large biomolecular assemblages that has provided impact in the study of a broad range of chemical, biological, and…

We present a new adaptive resolution technique for efficient particle-based multiscale molecular dynamics (MD) simulations. The presented approach is tailor-made for molecular systems where atomistic resolution is required only in spatially…

Combined-resolution simulations are an effective way to study molecular properties across a range of length- and time-scales. These simulations can benefit from adaptive boundaries that allow the high-resolution region to adapt (change size…

The complexity of biological systems and processes, spanning molecular to macroscopic scales, necessitates the use of multiscale simulations to get a comprehensive understanding. Quantum mechanics/molecular mechanics (QM/MM) molecular…

Recent advances in both theory and methods have created opportunities to simulate biomolecular processes more efficiently using adaptive ensemble simulations. Ensemble-based simulations are used widely to compute a number of individual…

Heterogeneous multiscale methods (HMM) combine molecular accuracy of particle-based simulations with the computational efficiency of continuum descriptions to model flow in soft matter liquids. In these schemes, molecular simulations…

Electronic structure simulation (ESS) has been used for decades to provide quantitative scientific insights on an atomistic scale, enabling advances in chemistry, biology, and materials science, among other disciplines. Following standard…

We present and discuss a framework for computer-aided multiscale analysis, which enables models at a "fine" (microscopic/stochastic) level of description to perform modeling tasks at a "coarse" (macroscopic, systems) level. These…

Recent advances in both theory and computational power have created opportunities to simulate biomolecular processes more efficiently using adaptive ensemble simulations. Ensemble simulations are now widely used to compute a number of…

Molecular simulations of the forced unfolding and refolding of biomolecules or molecular complexes allow to gain important kinetic, structural and thermodynamic information about the folding process and the underlying energy landscape. In…

Classical Molecular Dynamics (MD) simulations provide insight on the properties of many soft-matter systems. In some situations it is interesting to model the creation of chemical bonds, a process that is not part of the MD framework. In…

Enhanced sampling algorithms have emerged as powerful methods to extend the utility of molecular dynamics simulations and allow the sampling of larger portions of the configuration space of complex systems in a given amount of simulation…

We describe the adaptive resolution multiscale method AdResS. The conceptual evolution as well as the improvements of its technical efficiency are described step by step, with an explicit reference to current limitations and open problems.

Simulating physical systems is a core component of scientific computing, encompassing a wide range of physical domains and applications. Recently, there has been a surge in data-driven methods to complement traditional numerical simulations…

In a world made of atoms, the computer simulation of molecular systems, such as proteins in water, plays an enormous role in science. Software packages that perform these computations have been developed for decades. In molecular…