Journal of Computer-Aided Molecular Design

, Volume 30, Issue 11, pp 1067–1077

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

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

DOI: 10.1007/s10822-016-9961-9

Cite this article as:
Brini, E., Paranahewage, S.S., Fennell, C.J. et al. J Comput Aided Mol Des (2016) 30: 1067. doi:10.1007/s10822-016-9961-9


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 

Supplementary material

10822_2016_9961_MOESM1_ESM.pdf (1 mb)
Supplementary material 1 (pdf 1047 KB)

Funding information

Funder NameGrant NumberFunding Note
National Institutes of Health (US)
  • GM063592

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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