Efficient free energy calculation of water across lipid membranes

Keiko Shinoda, Wataru Shinoda, Masuhiro Mikami

Research output: Contribution to journalArticlepeer-review

22 Citations (Scopus)

Abstract

An efficient free energy (FE) calculation of a water molecule to go across lipid membranes is presented. Both overlapping distribution and cavity insertion Widom methods are complementarily used. The former is useful for a dense region where water molecules are found, i.e., from the interfacial to bulk water region, while the latter works well in the low density region, i.e., the hydrocarbon region. Since both methods evaluate the excess chemical potential of water, the obtained FE profile is free from the fitting problem usually arisen when a FE difference method is used. A diphytanyl phosphatidylcholine bilayer is used for our test calculations. An excellent and fast convergence of the chemical potential is obtained when each method is applied for the appropriate region. The estimated FE barrier using the Ewald method for the electrostatic interaction is ∼7.2 kcal/mol, which is higher than that using the interaction cutoff of 20 Åby about 0.9 kcal/mol.

Original languageEnglish
Pages (from-to)1912-1918
Number of pages7
JournalJournal of Computational Chemistry
Volume29
Issue number12
DOIs
Publication statusPublished - Sep 2008
Externally publishedYes

Keywords

  • Chemical potential
  • Free energy
  • Lipid membrane
  • Molecular dynamics
  • Water

ASJC Scopus subject areas

  • Chemistry(all)
  • Computational Mathematics

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