Journal of Computer-Aided Molecular Design

, Volume 30, Issue 11, pp 1067–1077 | Cite as

Adapting the semi-explicit assembly solvation model for estimating water-cyclohexane partitioning with the SAMPL5 molecules

  • Emiliano BriniEmail author
  • S. Shanaka Paranahewage
  • Christopher J. Fennell
  • Ken A. Dill


We describe here some tests we made in the SAMPL5 communal event of ‘Semi-Explicit Assembly’ (SEA), a recent method for computing solvation free energies. We combined the prospective tests of SAMPL5 with followup retrospective calculations, to improve two technical aspects of the field variant of SEA. First, SEA uses an approximate analytical surface around the solute on which a water potential is computed. We have improved and simplified the mathematical model of that surface. Second, some of the solutes in SAMPL5 were large enough to need a way to treat solvating waters interacting with ‘buried atoms’, i.e. interior atoms of the solute. We improved SEA with a buried-atom correction. We also compare SEA to Thermodynamic Integration molecular dynamics simulations, so that we can sort out force field errors.


SAMPL SEA Solvation free energy Partitioning Distribution coefficient 



The authors appreciate the support from National Institutes of Health Grants GM063592 and GM107104. Portions of the computing for this project were performed at the Laufer Center, XSEDE allocation CHE150012 to CJF, and the OSU High Performance Computing Center at Oklahoma State University supported in part through the National Science Foundation Grant OCI1126330.

Supplementary material

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Supplementary material 1 (pdf 1047 KB)


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Copyright information

© Springer International Publishing Switzerland 2016

Authors and Affiliations

  1. 1.Laufer Center for Physical and Quantitative BiologyStony Brook UniversityStony BrookUSA
  2. 2.Department of ChemistryOklahoma State UniversityStillwaterUSA
  3. 3.Department of ChemistryStony Brook UniversityStony BrookUSA
  4. 4.Department of Physics and AstronomyStony Brook UniversityStony BrookUSA

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