Continuum solvation of large molecules described by QM/MM: A semi-iterative implementation of the PCM/EFP interface

Hui Li, Christian S. Pomelli, Jan H. Jensen

Research output: Contribution to journalArticle

89 Citations (Scopus)

Abstract

The direct inversion of the iterative subspace (DIIS) solution to the iterative integral equation formalism polarized continuum model (IEF-PCM, 2001 Theor. Chem. Acc. 105:1186) is applied to the effective fragment potential IEF-PCM interface (2002 J Chem Phys 116:5023). Compared to a direct matrix-inversion solution, the DIIS-PCM is up to an order of magnitude more efficient both in computing time and memory requirements for large systems. Multipole treatments of long-range electrostatic interactions further reduce the computing tinge by up to 50%. All the CPU intensive computations are parallelized. The data presented in this paper demonstrate that use of the iterative IEF-PCM is an efficient way to model bulk solvation of large biomolecules described by QM/MM.

Original languageEnglish (US)
Pages (from-to)71-84
Number of pages14
JournalTheoretical Chemistry Accounts
Volume109
Issue number2
DOIs
StatePublished - Mar 1 2003

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Pulse code modulation
Solvation
solvation
inversions
continuums
Molecules
molecules
iterative solution
multipoles
integral equations
Biomolecules
Coulomb interactions
fragments
electrostatics
formalism
Integral equations
Program processors
requirements
matrices
Data storage equipment

Keywords

  • Continuum solvation
  • Polarized continuum model
  • Protein
  • Quantum mechanics/molecular mechanics

ASJC Scopus subject areas

  • Physical and Theoretical Chemistry

Cite this

Continuum solvation of large molecules described by QM/MM : A semi-iterative implementation of the PCM/EFP interface. / Li, Hui; Pomelli, Christian S.; Jensen, Jan H.

In: Theoretical Chemistry Accounts, Vol. 109, No. 2, 01.03.2003, p. 71-84.

Research output: Contribution to journalArticle

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