LAMMPS-a flexible simulation tool for particle-based materials modeling at the atomic, meso, and continuum scales
Since the classical molecular dynamics simulator LAMMPS was released as an open source
code in 2004, it has become a widely-used tool for particle-based modeling of materials at …
code in 2004, it has become a widely-used tool for particle-based modeling of materials at …
DeePMD-kit v2: A software package for deep potential models
DeePMD-kit is a powerful open-source software package that facilitates molecular dynamics
simulations using machine learning potentials known as Deep Potential (DP) models. This …
simulations using machine learning potentials known as Deep Potential (DP) models. This …
Learning molecular potentials with neural networks
The potential energy of molecular species and their conformers can be computed with a
wide range of computational chemistry methods, from molecular mechanics to ab initio …
wide range of computational chemistry methods, from molecular mechanics to ab initio …
n2v: A density‐to‐potential inversion suite. A sandbox for creating, testing, and benchmarking density functional theory inversion methods
Y Shi, VH Chávez, A Wasserman - Wiley Interdisciplinary …, 2022 - Wiley Online Library
From the most fundamental to the most practical side of density functional theory (DFT),
Kohn–Sham inversions (iKS) can contribute to the development of functional approximations …
Kohn–Sham inversions (iKS) can contribute to the development of functional approximations …
HspB8 prevents aberrant phase transitions of FUS by chaperoning its folded RNA-binding domain
EE Boczek, J Fürsch, ML Niedermeier, L Jawerth… - Elife, 2021 - elifesciences.org
Aberrant liquid-to-solid phase transitions of biomolecular condensates have been linked to
various neurodegenerative diseases. However, the underlying molecular interactions that …
various neurodegenerative diseases. However, the underlying molecular interactions that …
Parallel simulation via SPPARKS of on-lattice kinetic and Metropolis Monte Carlo models for materials processing
JA Mitchell, F Abdeljawad, C Battaile… - … and Simulation in …, 2023 - iopscience.iop.org
SPPARKS is an open-source parallel simulation code for developing and running various
kinds of on-lattice Monte Carlo models at the atomic or meso scales. It can be used to study …
kinds of on-lattice Monte Carlo models at the atomic or meso scales. It can be used to study …
A call to arms: Making the case for more reusable libraries
S Lehtola - The Journal of Chemical Physics, 2023 - pubs.aip.org
The traditional foundation of science lies on the cornerstones of theory and experiment.
Theory is used to explain experiment, which in turn guides the development of theory. Since …
Theory is used to explain experiment, which in turn guides the development of theory. Since …
PyDFT-QMMM: A modular, extensible software framework for DFT-based QM/MM molecular dynamics
JP Pederson, JG McDaniel - The Journal of Chemical Physics, 2024 - pubs.aip.org
PyDFT-QMMM is a Python-based package for performing hybrid quantum
mechanics/molecular mechanics (QM/MM) simulations at the density functional level of …
mechanics/molecular mechanics (QM/MM) simulations at the density functional level of …
LibERI—A portable and performant multi-GPU accelerated library for electron repulsion integrals via OpenMP offloading and standard language parallelism
A portable and performant graphics processing unit (GPU)-accelerated library for electron
repulsion integral (ERI) evaluation, named LibERI, has been developed and implemented …
repulsion integral (ERI) evaluation, named LibERI, has been developed and implemented …
[HTML][HTML] Multiscale biomolecular simulations in the exascale era
The complexity of biological systems and processes, spanning molecular to macroscopic
scales, necessitates the use of multiscale simulations to get a comprehensive …
scales, necessitates the use of multiscale simulations to get a comprehensive …