Semi-grand canonical molecular dynamics simulation of bovine pancreatic trypsin inhibitor

Gillian C. Lynch, Bernard Pettitt

Research output: Contribution to journalArticle

10 Citations (Scopus)

Abstract

In the quest to understand both the structural and thermodynamic facets of biomolecular-solvent systems semigrand canonical ensemble molecular dynamics simulations of a protein in solution are performed. In these simulations only the water molecules in the system are allowed to fluctuate; the final number of water molecules is determined by the chemical potential. An unbiased sampling technique is used for the insertion/deletion procedure of the water molecules thereby providing a benchmark grand ensemble simulation of the hydration structure of proteins. Three different chemical potential simulations were carried out offering a direct route to thermodynamic information from a molecular dynamics simulation. (C) 2000 Elsevier Science B.V.

Original languageEnglish (US)
Pages (from-to)405-413
Number of pages9
JournalChemical Physics
Volume258
Issue number2-3
DOIs
StatePublished - Aug 15 2000
Externally publishedYes

Fingerprint

trypsin
Aprotinin
inhibitors
Molecular dynamics
Chemical potential
molecular dynamics
Molecules
Water
Computer simulation
Thermodynamics
simulation
Hydration
water
Proteins
proteins
molecules
deletion
thermodynamics
Sampling
hydration

ASJC Scopus subject areas

  • Physical and Theoretical Chemistry
  • Spectroscopy
  • Atomic and Molecular Physics, and Optics

Cite this

Semi-grand canonical molecular dynamics simulation of bovine pancreatic trypsin inhibitor. / Lynch, Gillian C.; Pettitt, Bernard.

In: Chemical Physics, Vol. 258, No. 2-3, 15.08.2000, p. 405-413.

Research output: Contribution to journalArticle

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