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. 2024 Jul 3;64(14):5671–5679. doi: 10.1021/acs.jcim.4c00764

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© 2024 The Authors. Published by American Chemical Society

Permits non-commercial access and re-use, provided that author attribution and integrity are maintained; but does not permit creation of adaptations or other derivative works (https://creativecommons.org/licenses/by-nc-nd/4.0/).

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(A) The ligand structures of a transformation pair from L12 to L18 in the δ-opioid receptor are displayed along with the predicted ΔΔG values from both AMBER-TI and AToM-OpenMM, as well as experimental data. (B) The time evolution of the AMBER-TI and AToM-OpenMM results is illustrated by using accumulated simulation data, demonstrating convergence of the ΔΔG values. (C, D) The distribution of perturbation energy for the alchemical states with λ ranging from 0 to 1/2 using either 6 λ or 12 λ windows. Both figures show good overlaps between neighboring distributions. The color gradient indicates λ values, transitioning from red (0) to violet (1/2), following the rainbow color scheme.