LICHEM: A QM/MM Program for Simulations with Multipolar and Polarizable Force Fields

被引:79
作者
Kratz, Eric G. [1 ]
Walker, Alice R. [1 ]
Lagardere, Louis [2 ,3 ]
Lipparini, Filippo [4 ]
Piquemal, Jean-Philip [2 ,3 ]
Cisneros, G. Andres [1 ]
机构
[1] Wayne State Univ, Dept Chem, Detroit, MI 48202 USA
[2] Univ Paris 06, Chim Theor Lab, UMR 7617, F-75005 Paris, France
[3] Univ Paris 06, Inst Calcul & Simulat, F-75005 Paris, France
[4] Johannes Gutenberg Univ Mainz, Inst Phys Chem, Duesbergweg 10-14, D-55128 Mainz, Germany
基金
美国国家卫生研究院;
关键词
QM/MM; polarization; multipoles; pseudobond; AMOEBA; MINIMUM ENERGY PATHS; MOLECULAR-DYNAMICS SIMULATIONS; CLASSICAL DRUDE OSCILLATORS; FRAGMENT POTENTIAL METHOD; DNA-POLYMERASE-LAMBDA; SMALL WATER CLUSTERS; ELASTIC BAND METHOD; ENZYME-REACTIONS; HYBRID QM/MM; GEOMETRY OPTIMIZATION;
D O I
10.1002/jcc.24295
中图分类号
O6 [化学];
学科分类号
0703 ;
摘要
We introduce an initial implementation of the LICHEM software package. LICHEM can interface with Gaussian, PSI4, NWChem, TINKER, and TINKER-HP to enable QM/MM calculations using multipolar/polarizable force fields. LICHEM extracts forces and energies from unmodified QM and MM software packages to perform geometry optimizations, single-point energy calculations, or Monte Carlo simulations. When the QM and MM regions are connected by covalent bonds, the pseudo-bond approach is employed to smoothly transition between the QM region and the polarizable force field. A series of water clusters and small peptides have been employed to test our initial implementation. The results obtained from these test systems show the capabilities of the new software and highlight the importance of including explicit polarization. (C) 2016 Wiley Periodicals, Inc.
引用
收藏
页码:1019 / 1029
页数:11
相关论文
共 110 条
[1]  
Aida M, 2000, INT J QUANTUM CHEM, V77, P199, DOI 10.1002/(SICI)1097-461X(2000)77:1<199::AID-QUA19>3.0.CO
[2]  
2-T
[3]  
[Anonymous], ARXIV150505730
[4]  
[Anonymous], 2007, Numerical Recipes: The Art of Scientific Computing
[5]   A Hybrid QM/MM Simulation Study of Intramolecular Proton Transfer in the Pyridoxal 5′-Phosphate in the Active Site of Transaminase: Influence of Active Site Interaction on Proton Transfer [J].
Banik, Sindrila Dutta ;
Chandra, Amalendu .
JOURNAL OF PHYSICAL CHEMISTRY B, 2014, 118 (38) :11077-11089
[6]   Toward QM/MM Simulation of Enzymatic Reactions with the Drude Oscillator Polarizable Force Field [J].
Boulanger, Eliot ;
Thiel, Walter .
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 2014, 10 (04) :1795-1809
[7]   Solvent Boundary Potentials for Hybrid QM/MM Computations Using Classical Drude Oscillators: A Fully Polarizable Model [J].
Boulanger, Eliot ;
Thiel, Walter .
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 2012, 8 (11) :4527-4538
[8]   Achieving Linear Scaling in Computational Cost for a Fully Polarizable MM/Continuum Embedding [J].
Caprasecca, Stefano ;
Jurinovich, Sandro ;
Lagardere, Louis ;
Stamm, Benjamin ;
Lipparini, Filippo .
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 2015, 11 (02) :694-704
[9]   Geometry Optimization in Polarizable QM/MM Models: The Induced Dipole Formulation [J].
Caprasecca, Stefano ;
Jurinovich, Sandro ;
Viani, Lucas ;
Curutchet, Carles ;
Mennucci, Benedetta .
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 2014, 10 (04) :1588-1598
[10]   Toward a Unified Modeling of Environment and Bridge-Mediated Contributions to Electronic Energy Transfer: A Fully Polarizable QM/MM/PCM Approach [J].
Caprasecca, Stefano ;
Curutchet, Carles ;
Mennucci, Benedetta .
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 2012, 8 (11) :4462-4473