Journal of Computer-Aided Molecular Design

, Volume 30, Issue 11, pp 1045–1058 | Cite as

Prediction of cyclohexane-water distribution coefficients for the SAMPL5 data set using molecular dynamics simulations with the OPLS-AA force field



All-atom molecular dynamics simulations were used to predict water-cyclohexane distribution coefficients \(D_{cw}\) of a range of small molecules as part of the SAMPL5 blind prediction challenge. Molecules were parameterized with the transferable all-atom OPLS-AA force field, which required the derivation of new parameters for sulfamides and heterocycles and validation of cyclohexane parameters as a solvent. The distribution coefficient was calculated from the solvation free energies of the compound in water and cyclohexane. Absolute solvation free energies were computed by an established protocol using windowed alchemical free energy perturbation with thermodynamic integration. This protocol resulted in an overall root mean square error in \(\log D_{cw}\) of almost 4 log units and an overall signed error of −3 compared to experimental data. There was no substantial overall difference in accuracy between simulating in NVT and NPT ensembles. The signed error suggests a systematic error but the experimental \(D_{cw}\) data on their own are insufficient to uncover the source of this error. Preliminary work suggests that the major source of error lies in the hydration free energy calculations.


Molecular dynamics Solvation free energy OPLS-AA force field Ligand parameterization Free energy perturbation Thermodynamic integration Cyclohexane-water distribution coefficients 



OB was supported in part by Grant ACI-1443054 from the National Science Foundation. BII was supported in part by Grants ANR-10-LABX-33 (LabEx LERMIT) and ANR-14-JAMR-0002-03 (JPIAMR) from the French National Research Agency (ANR).

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Copyright information

© Springer International Publishing Switzerland 2016

Authors and Affiliations

  1. 1.Department of PhysicsArizona State UniversityTempeUSA
  2. 2.Center for Biological PhysicsArizona State UniversityTempeUSA
  3. 3.Institut de Chimie des Substances Naturelles, CNRS UPR 2301Université Paris-Saclay, Labex LERMITGif-sur-YvetteFrance

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