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physics.comp-ph2026
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…
physics.comp-ph2026★ 2 cited
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…
physics.comp-ph2024
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…