Related papers: Computational Efficiency and Amdahl's law for the …
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…
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…
This paper reinterprets Amdahl's law in terms of execution time and applies this simple model to supercomputing. The systematic discussion results in practical formulas enabling to calculate expected running time using large number of…
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…
For simulation studies of (macro) molecular liquids it would be of significant interest to be able to adjust or increase the level of resolution within one region of space, while allowing for the free exchange of molecules between open…
The problem of learning parallel computer performance is investigated in the context of multicore processors. Given a fixed workload, the effect of varying system configuration on performance is sought. Conventionally, the performance…
Quantum simulation of chemical systems is one of the most promising near-term applications of quantum computers. The variational quantum eigensolver, a leading algorithm for molecular simulations on quantum hardware, has a serious…
Adaptive Molecular Resolution approaches in Molecular Dynamics are becoming relevant tools for the analysis of molecular liquids characterized by the interplay of different physical scales. The essential difference among these methods is in…
Numerical solutions to fractional differential equations can be extremely computationally intensive due to the effect of non-local derivatives in which all previous time points contribute to the current iteration. In finite difference…
-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…
We present a multiscale simulation of liquid water where a spatially adaptive molecular resolution procedure allows for changing on-the-fly from a coarse-grained to an all-atom representation. We show that this approach leads to the correct…
Simulation schemes that allow to change molecular representation in a subvolume of the simulation box while preserving the equilibrium with the surrounding introduce conceptual problems of thermodynamic consistency. In this work we present…
Obtainable computational efficiency is evaluated when using an Adaptive Mesh Refinement (AMR) strategy in time accurate simulations governed by sets of conservation laws. For a variety of 1D, 2D, and 3D hydro- and magnetohydrodynamic…
Chemical accuracy serves as an important metric for assessing the effectiveness of the numerical method in Kohn--Sham density functional theory. It is found that to achieve chemical accuracy, not only the Kohn--Sham wavefunctions but also…
Molecular dynamics simulates the~movements of atoms. Due to its high cost, many methods have been developed to "push the~simulation forward". One of them, metadynamics, can hasten the~molecular dynamics with the~help of variables describing…
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.
The modification of Amdahl's law for the case of increment of processor elements in a computer system is considered. The coefficient $k$ linking accelerations of parallel and parallel specialized computer systems is determined. The limiting…
Large-scale atomistic simulations rely on interatomic potentials providing an efficient representation of atomic energies and forces. Modern machine-learning (ML) potentials provide the most precise representation compared to electronic…
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…
Complex soft matter systems can be efficiently studied with the help of adaptive resolution simulation methods, concurrently employing two levels of resolution in different regions of the simulation domain. The non-matching properties of…