相关论文: Adaptive Resolution Simulation in Equilibrium and …
The adaptive resolution simulation (AdResS) technique couples regions with different molecular resolutions and allows the exchange of molecules between different regions in an adaptive fashion. The latest development of the technique allows…
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.
We extend the application of the adaptive resolution technique (AdResS) to liquid systems composed of alkane chains of different lengths. The aim of the study is to develop and test the modifications of AdResS required in order to handle…
The Adaptive Resolution Scheme (AdResS) is a hybrid scheme that allows one to treat a molecular system with different levels of resolution depending on the location of the molecules. The construction of a Hamiltonian based on the this idea…
We employ the adaptive resolution approach AdResS, in its recently developed Grand Canonical-like version (GC-AdResS) [Wang et al. Phys.Rev.X 3, 011018 (2013)], to calculate the excess chemical potential, $\mu^{ex}$, of various liquids and…
We present a dual-resolution molecular dynamics (MD) simulation of liquid water employing a recently introduced Adaptive Resolution Scheme (AdResS). The spatially adaptive molecular resolution procedure allows for changing from a…
The recently proposed Hamiltonian Adaptive Resolution Scheme (H-AdResS) allows to perform molecular simulations in an open boundary framework. It allows to change on the fly the resolution of specific subset of molecules (usually the…
In this work, we provide a detailed theoretical analysis, supported by numerical tests, of the reliability of the adaptive resolution simulation (AdResS) technique in sampling the Grand Canonical ensemble. We demonstrate that the correct…
In a previous paper [Gholami et al. Adv.Th.Sim.4, 2000303 (2021)], we have identified a precise relation between the chemical potential of a fully atomistic simulation and the simulation of an open system in the adaptive resolution method…
Many natural phenomena involve processes that happen simultaneously at different characteristic length- and timescales. Typically, the region where the process of interest happens is affected by fluctuations in its surroundings. Modeling…
We consider the theoretical model of Bergmann and Lebowitz for open systems out of equilibrium and translate its principles in the adaptive resolution molecular dynamics technique (AdResS). We simulate Lennard-Jones fluids with open…
Recently, a novel type of a multiscale simulation, called Relative Resolution (RelRes), was introduced. In a single system, molecules switch their resolution in terms of their relative separation, with near neighbors interacting via…
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…
We have implemented the Centroid Molecular Dynamics scheme (CMD) into the Grand Canonical-like version of the Adaptive Resolution Simulation Molecular Dynamics (GC-AdResS) method. We have tested the implementation on two different systems,…
Fluid transport across nanometric channels induced by electric, pressure and concentration gradients is ubiquitous in biological systems and fosters various applications. In this context, computer simulation setups with well-defined…
In molecular simulation and fluid mechanics, the coupling of a particle domain with a continuum representation of its embedding environment is an ongoing challenge. In this work, we show a novel approach where the latest version of the…
We extend the use of the adaptive resolution method (AdResS) in its Grand Canonical-like version (GC-AdResS) to the molecular dynamics simulation of 1,3-dimethylimidazolium chloride. We show that the partitioning of the total system in a…
Recently, we introduced Relative Resolution as a hybrid formalism for fluid mixtures [1]. The essence of this approach is that it switches molecular resolution in terms or relative separation: While nearest neighbors are characterized by a…
The unfolding of molecular complexes or biomolecules under the influence of external mechanical forces can routinely be simulated with atomistic resolution. To obtain a match of the characteristic time scales with those of experimental…
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…