4 papers · 1 filter
Development and large-scale benchmarks of a protein--ligand absolute binding free energy toolkit
Yu Liu, Ailun Wang, Yu Xia +2
Absolute binding free energy (ABFE) calculations offer a theoretically rigorous approach for predicting protein--ligand binding affinities without the scaffold constraints of relat…
Bridging Quantum Mechanics to Organic Liquid Properties via a Universal Force Field
Tianze Zheng, Xingyuan Xu, Zhi Wang +10
Molecular dynamics (MD) simulations are essential tools for unraveling atomistic insights into the structure and dynamics of condensed-phase systems. However, the universal and acc…
OpenMM-Python-Force: Deploying Accelerated Python Modules in Molecular Dynamics Simulation
Zhi Wang, Wen Yan
We present OpenMM-Python-Force, a plugin designed to extend OpenMM's functionality by enabling integration of energy and force calculations from external Python programs via a call…
Enhancing GPU-acceleration in the Python-based Simulations of Chemistry Framework
Xiaojie Wu, Qiming Sun, Zhichen Pu +11
We describe our contribution as industrial stakeholders to the existing open-source GPU4PySCF project (https: //github.com/pyscf/gpu4pyscf), a GPU-accelerated Python quantum chemis…