Quantum Fragment Based ab Initio Molecular Dynamics for Proteins

Jinfeng Liu, Tong Zhu, Xianwei Wang, Xiao He, John Zhang

Research output: Contribution to journalArticle

Abstract

Developing ab initio molecular dynamics (AIMD) methods for practical application in protein dynamics is of significant interest. Due to the large size of biomolecules, applying standard quantum chemical methods to compute energies for dynamic simulation is computationally prohibitive. In this work, a fragment based ab initio molecular dynamics approach is presented for practical application in protein dynamics study. In this approach, the energy and forces of the protein are calculated by a recently developed electrostatically embedded generalized molecular fractionation with conjugate caps (EE-GMFCC) method. For simulation in explicit solvent, mechanical embedding is introduced to treat protein interaction with explicit water molecules. This AIMD approach has been applied to MD simulations of a small benchmark protein Trpcage (with 20 residues and 304 atoms) in both the gas phase and in solution. Comparison to the simulation result using the AMBER force field shows that the AIMD gives a more stable protein structure in the simulation, indicating that quantum chemical energy is more reliable. Importantly, the present fragment-based AIMD simulation captures quantum effects including electrostatic polarization and charge transfer that are missing in standard classical MD simulations. The current approach is linear-scaling, trivially parallel, and applicable to performing the AIMD simulation of proteins with a large size.

Original languageEnglish (US)
Pages (from-to)5897-5905
Number of pages9
JournalJournal of Chemical Theory and Computation
Volume11
Issue number12
DOIs
StatePublished - Oct 23 2015

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Molecular dynamics
fragments
molecular dynamics
proteins
Proteins
simulation
Computer simulation
chemical energy
Biomolecules
Fractionation
Charge transfer
Electrostatics
caps
fractionation
embedding
field theory (physics)
Gases
Polarization
charge transfer
Atoms

ASJC Scopus subject areas

  • Physical and Theoretical Chemistry
  • Computer Science Applications

Cite this

Quantum Fragment Based ab Initio Molecular Dynamics for Proteins. / Liu, Jinfeng; Zhu, Tong; Wang, Xianwei; He, Xiao; Zhang, John.

In: Journal of Chemical Theory and Computation, Vol. 11, No. 12, 23.10.2015, p. 5897-5905.

Research output: Contribution to journalArticle

Liu, Jinfeng ; Zhu, Tong ; Wang, Xianwei ; He, Xiao ; Zhang, John. / Quantum Fragment Based ab Initio Molecular Dynamics for Proteins. In: Journal of Chemical Theory and Computation. 2015 ; Vol. 11, No. 12. pp. 5897-5905.
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