Related papers: fix pimd/langevin: An Efficient Implementation of …
Nuclear quantum effects (NQEs) play an essential role in many atomistic systems, yet their explicit inclusion in molecular simulations remains challenging. Path-integral molecular dynamics (PIMD) provides a rigorous framework for…
It is now established that nuclear quantum motion plays an important role in determining water's hydrogen bonding, structure, and dynamics. Such effects are important to include in density functional theory (DFT) based molecular dynamics…
The quantum nature of nuclei plays an important role in the accurate modelling of light atoms such as hydrogen, but it is often neglected in simulations due to the high computational overhead involved. It has recently been shown that…
Path integral-based simulation methodologies play a crucial role for the investigation of nuclear quantum effects by means of computer simulations. However, these techniques are significantly more demanding than corresponding classical…
Machine learning potentials have emerged as a means to enhance the accuracy of biomolecular simulations. However, their application is constrained by the significant computational cost arising from the vast number of parameters compared to…
This paper introduces a random-batch molecular dynamics (RBMD) package for fast simulations of particle systems at the nano/micro scale. Different from existing packages, the RBMD uses random batch methods for nonbonded interactions of…
Bosonic exchange symmetry leads to fascinating quantum phenomena, from exciton condensation in quantum materials to the superfluidity of liquid Helium-4. Unfortunately, path integral molecular dynamics (PIMD) simulations of bosons are…
Building on Paper I of this series, which introduced path integral Monte Carlo (PIMC) estimators for the derivative of the potential of mean force (PMF), we propose two path integral molecular dynamics (PIMD) integrators that can make use…
We introduce mapping-variable ring polymer molecular dynamics (MV-RPMD), a model dynamics for the direct simulation of multi-electron processes. An extension of the RPMD idea, this method is based on an exact, imaginary time path-integral…
Langevin dynamics sampling suffers from extremely low generation speed, fundamentally limited by numerous fine-grained iterations to converge to the target distribution. We introduce PID-controlled Langevin Dynamics (PIDLD), a novel…
With the rapid advancement of computational techniques, Molecular Dynamics (MD) simulations have emerged as powerful tools in biomedical research, enabling in-depth investigations of biological systems at the atomic level. Among the diverse…
Ring polymer molecular dynamics (RPMD) is used to directly simulate the dynamics of an excess electron in a supercritical fluid over a broad range of densities. The accuracy of the RPMD model is tested against numerically exact path…
For 35 years, {\it ab initio} molecular dynamics (AIMD) has been the method of choice for modeling complex atomistic phenomena from first principles. However, most AIMD applications are limited by computational cost to systems with…
Bulk-bitwise processing-in-memory (PIM), where large bitwise operations are performed in parallel by the memory array itself, is an emerging form of computation with the potential to mitigate the memory wall problem. This paper examines the…
The contribution of nuclear quantum effects (NQEs) to the properties of various hydrogen-bound systems, including biomolecules, is increasingly recognized. Despite the development of many acceleration techniques, the computational overhead…
DL_POLY Quantum 2.1 is introduced here as a highly modular, sustainable, and scalable general-purpose molecular dynamics (MD) simulation software for large-scale long-time MD simulations of condensed phase and interfacial systems with the…
It is well known that the number of particles should be scaled up to enable industrial scale simulation. The calculations are more computationally intensive when the motion of the surrounding fluid is considered. Besides the advances in…
In this paper, we propose a cost-reduced method for finite-temperature molecular dynamics on a near-term quantum computer, Quantum Car-Parrinello molecular dynamics (QCPMD). One of the most promising applications of near-term quantum…
Developing efficient path integral (PI) methods for atomistic simulations of vibrational spectra in heterogeneous condensed phases and interfaces has long been a challenging task. Here, we present the h-CMD method, short for hybrid centroid…
Classical and path integral molecular dynamics (PIMD) simulations are used to study alpha-quartz and beta-quartz in a large range of temperatures at zero external stress. PIMD account for quantum fluctuations of atomic vibrations, which can…