ArticleJournal of computer-aided molecular design2021
Precise force-field-based calculations of octanol-water partition coefficients for the SAMPL7 molecules.
Article in Journal of computer-aided molecular design, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 4 papers.
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4 citing papers in PubMed.
- IMERGE-FEP: Improving Relative Free Energy Calculation Convergence with Chemical Intermediates.The journal of physical chemistry. B · 2025Article
- Calculated hydration free energies become less accurate with increases in molecular weight.PloS one · 2024Article
- Predicting octanol/water partition coefficients using molecular simulation for the SAMPL7 challenge: comparing the use of neat and water saturated 1-octanol.Journal of computer-aided molecular design · 2021Article
- Evaluation of log P, pKJournal of computer-aided molecular design · 2021Article
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5 authors.
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Abstract
We predicted water-octanol partition coefficients for the molecules in the SAMPL7 challenge with explicit solvent classical molecular dynamics (MD) simulations. Water hydration free energies and octanol solvation free energies were calculated with a windowed alchemical free energy approach. Three commonly used force fields (AMBER GAFF, CHARMM CGenFF, OPLS-AA) were tested. Special emphasis was placed on converging all simulations, using a criterion developed for the SAMPL6 challenge. In aggregate, over 1000 [Formula: see text]s of simulations were performed, with some free energy windows remaining not fully converged even after 1 [Formula: see text]s of simulation time. Nevertheless, the amount of sampling produced [Formula: see text] estimates with a precision of 0.1 log units or better for converged simulations. Despite being probably as fully sampled as can expected and is feasible, the agreement with experiment remained modest for all force fields, with no force field performing better than 1.6 in root mean squared error. Overall, our results indicate that a large amount of sampling is necessary to produce precise [Formula: see text] predictions for the SAMPL7 compounds and that high precision does not necessarily lead to high accuracy. Thus, fundamental problems remain to be solved for physics-based [Formula: see text] predictions.
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