The implementation of a fast and accurate QM/MM potential method in Amber

Ross C. Walker, Ichael F. Crowley, David A. Case

Research output: Contribution to journalArticle

233 Scopus citations

Abstract

Version 9 of the Amber simulation programs includes a new semi-empirical hybrid QM/MM functionality. This includes support for implicit solvent (generalized Born) and for periodic explicit solvent simulations using a newly developed QM/MM implementation of the particle mesh Ewald (PME) method. The code provides sufficiently accurate gradients to run constant energy QM/MM MD simulations for many nanoseconds. The link atom approach used for treating the QM/MM boundary shows improved performance, and the user interface has been rewritten to bring the format into line with classical MD simulations. Support is provided for the PM3, PDDG/PM3, PM3CARB1, AMI, MNDO, and PDDG/MNDO semi-empirical Hamiltonians as well as the self-consistent charge density functional tight binding (SCC-DFTB) method. Performance has been improved to the point where using QM/MM, for a QM system of 71 atoms within an explicitly solvated protein using periodic boundaries and PME requires less than twice the cpu time of the corresponding classical simulation.

Original languageEnglish (US)
Pages (from-to)1019-1031
Number of pages13
JournalJournal of Computational Chemistry
Volume29
Issue number7
DOIs
StatePublished - May 1 2008
Externally publishedYes

All Science Journal Classification (ASJC) codes

  • Chemistry(all)
  • Computational Mathematics

Keywords

  • Amber
  • Ewald
  • MD
  • Molecular dynamics
  • Molecular mechanics
  • PME
  • Particle mesh Ewald
  • QM/MM
  • Quantum mechanics

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