title: Quantum Fragment Based ab Initio Molecular Dynamics for Proteins.
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.
authors.affiliation: State Key Laboratory of Precision Spectroscopy, Institute of Theoretical and Computational Science, East China Normal University , Shanghai 200062, China.
authors.forename: Jinfeng
authors.initials: J
authors.lastname: Liu
authors.affiliation: State Key Laboratory of Precision Spectroscopy, Institute of Theoretical and Computational Science, East China Normal University , Shanghai 200062, China.|NYU-ECNU Center for Computational Chemistry at NYU Shanghai, Shanghai 200062, China.
authors.forename: Tong
authors.initials: T
authors.lastname: Zhu
authors.affiliation: Center for Optics & Optoelectronics Research, College of Science, Zhejiang University of Technology , Hangzhou, Zhejiang 310023, China.
authors.forename: Xianwei
authors.initials: X
authors.lastname: Wang
authors.affiliation: State Key Laboratory of Precision Spectroscopy, Institute of Theoretical and Computational Science, East China Normal University , Shanghai 200062, China.|NYU-ECNU Center for Computational Chemistry at NYU Shanghai, Shanghai 200062, China.
authors.forename: Xiao
authors.initials: X
authors.lastname: He
authors.affiliation: State Key Laboratory of Precision Spectroscopy, Institute of Theoretical and Computational Science, East China Normal University , Shanghai 200062, China.|NYU-ECNU Center for Computational Chemistry at NYU Shanghai, Shanghai 200062, China.|Department of Chemistry, New York University , New York, New York 10003, United States.
authors.forename: John Z H
authors.initials: JZ
authors.lastname: Zhang
mesh_terms: D005740:Gases / Q000737:chemistry; D056004:Molecular Dynamics Simulation; D017434:Protein Structure, Tertiary; D011506:Proteins / Q000737:chemistry*; D011789:Quantum Theory; D055672:Static Electricity; D014867:Water / Q000737:chemistry
chemical_list: D005740:Gases; D011506:Proteins; D014867:Water