Journal of Computer-Aided Molecular Design

, Volume 28, Issue 8, pp 825–829 | Cite as

Box size effects are negligible for solvation free energies of neutral solutes

  • Sreeja Parameswaran
  • David L. MobleyEmail author


Hydration free energy calculations in explicit solvent have become an integral part of binding free energy calculations and a valuable test of force fields. Most of these simulations follow the conventional norm of keeping edge length of the periodic solvent box larger than twice the Lennard-Jones (LJ) cutoff distance, with the rationale that this should be sufficient to keep the interactions between copies of the solute to a minimum. However, for charged solutes, hydration free energies can exhibit substantial box size-dependence even at typical box sizes. Here, we examine whether similar size-dependence affects hydration of neutral molecules. Thus, we focused on two strongly polar molecules with large dipole moments, where any size-dependence should be most pronounced, and determined how their hydration free energies vary as a function of simulation box size. In addition to testing a variety of simulation box sizes, we also tested two LJ cut-off distances, 0.65 and 1.0 nm. We show from these simulations that the calculated hydration free energy is independent of the box-size as well as the LJ cut-off distance, suggesting that typical hydration free energy calculations of neutral compounds indeed need not be particularly concerned with finite-size effects as long as standard good practices are followed.


Hydration free energy Box size Free energy calculation 

Supplementary material

10822_2014_9766_MOESM1_ESM.pdf (46 kb)
Supplementary material 1 (pdf 46 KB)


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Copyright information

© Springer International Publishing Switzerland 2014

Authors and Affiliations

  1. 1.Department of Pharmaceutical Sciences and Department of ChemistryUniversity of California, IrvineIrvineUSA
  2. 2.Department of ChemistryUniversity of New OrleansNew OrleansUSA

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