A force balanced fragmentation method for ab initio molecular dynamic simulation of protein

Mingyuan Xu, Tong Zhu, John Zhang

Research output: Contribution to journalArticle

Abstract

A force balanced generalized molecular fractionation with conjugate caps (FB-GMFCC) method is proposed for ab initio molecular dynamic simulation of proteins. In this approach, the energy of the protein is computed by a linear combination of the QM energies of individual residues and molecular fragments that account for the two-body interaction of hydrogen bond between backbone peptides. The atomic forces on the caped H atoms were corrected to conserve the total force of the protein. Using this approach, ab initio molecular dynamic simulation of an Ace-(ALA)9-NME linear peptide showed the conservation of the total energy of the system throughout the simulation. Further a more robust 110 ps ab initio molecular dynamic simulation was performed for a protein with 56 residues and 862 atoms in explicit water. Compared with the classical force field, the ab initio molecular dynamic simulations gave better description of the geometry of peptide bonds. Although further development is still needed, the current approach is highly efficient, trivially parallel, and can be applied to ab initio molecular dynamic simulation study of large proteins.

Original languageEnglish (US)
Article number189
JournalFrontiers in Chemistry
Volume6
Issue numberMAY
DOIs
StatePublished - May 1 2018

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Molecular dynamics
Computer simulation
Proteins
Peptides
Atoms
Fractionation
Conservation
Hydrogen bonds
Geometry
Water

Keywords

  • Ab initio molecular dynamics
  • Force balanced
  • GB3
  • MFCC
  • Protein dynamics
  • Quantum fragment method

ASJC Scopus subject areas

  • Chemistry(all)

Cite this

A force balanced fragmentation method for ab initio molecular dynamic simulation of protein. / Xu, Mingyuan; Zhu, Tong; Zhang, John.

In: Frontiers in Chemistry, Vol. 6, No. MAY, 189, 01.05.2018.

Research output: Contribution to journalArticle

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