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Front. Chem. | doi: 10.3389/fchem.2018.00189

A Force Balanced Fragmentation Method for Ab Initio Molecular Dynamics Simulation of Protein

Ming Y. Xu1,  Tong Zhu1, 2* and  John Z. Zhang1, 2, 3*
  • 1East China Normal University, China
  • 2New York University Shanghai, China
  • 3New York University, United States

A force balanced generalized molecular fractionation with conjugate caps (FB-GMFCC) method is proposed for ab initio molecular dynamics 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 dynamics 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 110ps ab initio molecular dynamics 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 dynamics 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 dynamics simulation study of large proteins.

Keywords: quantum fragment method, ab initio molecular dynamics, Force balanced, Gb3, protein dynamics, MFCC

Received: 06 Mar 2018; Accepted: 09 May 2018.

Edited by:

Thomas S. Hofer, University of Innsbruck, Austria

Reviewed by:

Hans M. Senn, University of Glasgow, United Kingdom
Antonio Monari, Université de Lorraine, France  

Copyright: © 2018 Xu, Zhu and Zhang. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

* Correspondence:
Prof. Tong Zhu, East China Normal University, Shanghai, China, tzhu@lps.ecnu.edu.cn
Prof. John Z. Zhang, East China Normal University, Shanghai, China, john.zhang@nyu.edu