BFEE2: Automated, Streamlined, and Accurate Absolute Binding Free-Energy Calculations.
Generalizing the Discrete Gibbs Sampler-Based λ-Dynamics Approach for Multisite Sampling of Many Ligands.
#NAMD ALCHEMISTRY TUTORIAL FREE#
Machine Learning and Enhanced Sampling Simulations for Computing the Potential of Mean Force and Standard Binding Free Energy. Martina Bertazzo, Dorothea Gobbo, Sergio Decherchi, Andrea Cavalli.Global Optimization of the Lennard-Jones Parameters for the Drude Polarizable Force Field. Computational Approaches for Protein pK a Calculations. Journal of Chemical Information and Modeling 2023, 63 TIES 2.0: A Dual-Topology Open Source Relative Binding Free Energy Builder with Web Portal. This article is cited by 22 publications.
#NAMD ALCHEMISTRY TUTORIAL CODE#
The new FEP-enabled code has been released with NAMD 3.0. Through optimized GPU performance, the present developments provide the community with a cost-effective solution for conducting FEP calculations. Moreover, we have extended this new FEP implementation to a code path highly optimized for a single-GPU node, which proves to be up to nearly 30 times faster than the CPU implementation. Compared to the CPU implementation available since 2001 in NAMD, our benchmarks indicate that the new implementation of FEP in traditional GPU code is about four times faster, without any noticeable loss of accuracy, thereby paving the way toward more affordable free-energy calculations on large biological objects. We report a new GPU-based implementation in NAMD of free-energy perturbation (FEP), one of the oldest, most popular importance-sampling approaches for the determination of free-energy differences that underlie alchemical transformations. Harnessing the power of graphics processing units (GPUs) to accelerate molecular dynamics (MD) simulations in the context of free-energy calculations has been a longstanding effort toward the development of versatile, high-performance MD engines.
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