Interfacing the Core-Shell or the Drude Polarizable Force Field With Car-Parrinello Molecular Dynamics for QM/MM Simulations

被引:18
|
作者
Sahoo, Sudhir K. [1 ,2 ]
Nair, Nisanth N. [1 ]
机构
[1] Indian Inst Technol Kanpur, Dept Chem, Kanpur, Uttar Pradesh, India
[2] Univ Paderborn, Dept Chem, Paderborn, Germany
来源
FRONTIERS IN CHEMISTRY | 2018年 / 6卷
关键词
QMMM simulations; MD; POLARIZED MM; catalysis; CPMD-GULP; AB-INITIO; HYDROGEN-EXCHANGE; PROTON-EXCHANGE; ALPHA-QUARTZ; ALKANE; MODEL; ACTIVATION; CHARMM; OSCILLATORS; TEMPERATURE;
D O I
10.3389/fchem.2018.00275
中图分类号
O6 [化学];
学科分类号
0703 ;
摘要
We report a quantum mechanics/polarizable-molecular mechanics (QM/p-MM) potential based molecular dynamics (MD) technique where the core-shell (or the Drude) type polarizable MM force field is interfaced with the plane-wave density functional theory based QM force field which allows Car-Parrinello MD for the QM subsystem. In the QM/p-MM Lagrangian proposed here, the shell (or the Drude) MM variables are treated as extended degrees of freedom along with the Kohn-Sham (KS) orbitals describing the QM wavefunction. The shell and the KS orbital degrees of freedom are then adiabatically decoupled from the nuclear degrees of freedom. In this respect, we also present here the Nose-Hoover Chain thermostat implementation for the dynamical subsystems. Our approach is then used to investigate the effect of MM polarization on the QM/MM results. Especially, the consequence of MM polarization on reaction free energy barriers, defect formation energy, and structural and dynamical properties are investigated. A low point charge polarizable potential (p-MZHB) for pure siliceous systems is also reported here.
引用
收藏
页数:10
相关论文
共 50 条
  • [21] A Hamiltonian electrostatic coupling scheme for hybrid Car-Parrinello molecular dynamics simulations
    Laio, A
    VandeVondele, J
    Rothlisberger, U
    JOURNAL OF CHEMICAL PHYSICS, 2002, 116 (16): : 6941 - 6947
  • [22] A Polarizable Force Field of Dipalmitoylphosphatidylcholine Based on the Classical Drude Model for Molecular Dynamics Simulations of Lipids
    Chowdhary, Janamejaya
    Harder, Edward
    Lopes, Pedro E. M.
    Huang, Lei
    MacKerell, Alexander D., Jr.
    Roux, Benoit
    JOURNAL OF PHYSICAL CHEMISTRY B, 2013, 117 (31): : 9142 - 9160
  • [23] Car-Parrinello Molecular Dynamics Simulations of Microstructure Properties of Liquid Water, Methanol and Ethanol
    Zeng Yong-Ping
    Zhu Xiao-Min
    Yang Zheng-Hua
    ACTA PHYSICO-CHIMICA SINICA, 2011, 27 (12) : 2779 - 2785
  • [24] Investigating biological systems using first principles Car-Parrinello molecular dynamics simulations
    Dal Peraro, Matteo
    Ruggerone, Paolo
    Raugei, Simone
    Gervasio, Francesco Luigi
    Carloni, Paolo
    CURRENT OPINION IN STRUCTURAL BIOLOGY, 2007, 17 (02) : 149 - 156
  • [25] Sampling phase space by a combined QM/MM ab initio Car-Parrinello molecular dynamics method with different (multiple) time steps in the quantum mechanical (QM) and molecular mechanical (MM) domains
    Woo, TK
    Margl, P
    Blöchl, PE
    Ziegler, T
    JOURNAL OF PHYSICAL CHEMISTRY A, 2002, 106 (07): : 1173 - 1182
  • [26] QM/MM Car-Parrinello molecular dynamics study of the solvent effects on the ground state and on the first excited singlet state of acetone in water
    Röhrig, UF
    Frank, I
    Hutter, J
    Laio, A
    VandeVondele, J
    Rothlisberger, U
    CHEMPHYSCHEM, 2003, 4 (11) : 1177 - 1182
  • [27] Cisplatin binding to DNA oligomers from hybrid Car-Parrinello/molecular dynamics simulations
    Spiegel, K
    Rothlisberger, U
    Carloni, P
    JOURNAL OF PHYSICAL CHEMISTRY B, 2004, 108 (08): : 2699 - 2707
  • [28] Car-Parrinello molecular dynamics simulations of Na+ solvation in water, methanol and ethanol
    Zeng, Yongping
    Hu, Junmei
    Yuan, Yu
    Zhang, Xiaobin
    Ju, Shengui
    CHEMICAL PHYSICS LETTERS, 2012, 538 : 60 - 66
  • [29] Sodium migration pathways in multicomponent silicate glasses: Car-Parrinello molecular dynamics simulations
    Tilocca, Antonio
    JOURNAL OF CHEMICAL PHYSICS, 2010, 133 (01):
  • [30] Molecular dynamics simulations using the drude polarizable force field on GPUs with OpenMM: Implementation, validation, and benchmarks
    Huang, Jing
    Lemkul, Justin A.
    Eastman, Peter K.
    MacKerell, Alexander D., Jr.
    JOURNAL OF COMPUTATIONAL CHEMISTRY, 2018, 39 (21) : 1682 - 1689