Efficient evaluation of electrostatic potential with computerized optimized code

被引:1229
作者
Zhang, Jun [1 ]
Lu, Tian [2 ]
机构
[1] Shenzhen Bay Lab, Inst Syst & Phys Biol, Shenzhen 518055, Peoples R China
[2] Beijing Kein Res Ctr Nat Sci, Beijing 100022, Peoples R China
关键词
ATOMIC CHARGES; BIOLOGICAL INTERFACES; MOLECULAR-MECHANICS; AM1-BCC MODEL; FREE-ENERGIES; WAVE-FUNCTION; SURFACE; GENERATION; QUALITY; TEMPERATURE;
D O I
10.1039/d1cp02805g
中图分类号
O64 [物理化学(理论化学)、化学物理学];
学科分类号
070304 ; 081704 ;
摘要
The evaluation of molecular electrostatic potential (ESP) is a performance bottleneck for many computational chemical tasks like restrained ESP charge fitting or quantum mechanics/molecular mechanics simulations. In this paper, an efficient algorithm for the evaluation of ESP is proposed. It regroups the expression in terms of primitive Gaussian type orbitals (GTOs) with identical angular momentum types and nuclei centers. Each term is calculated using a computerized optimized code. This algorithm was integrated into the wavefunction analysis program Multiwfn and was tested on several large systems. In the cases of dopamine and remdesivir, the performance of this algorithm was comparable to or better than some popular state-of-the-art codes. For meta1-organic framework-5, where the number of GTOs and ESP points is 4840 and 259 262, respectively, our code could finish the evaluation in 1874 seconds on ordinary hardware. It also exhibits good parallelization scaling. The source code of this algorithm is freely available and can become a useful tool for computational chemists.
引用
收藏
页码:20323 / 20328
页数:6
相关论文
共 48 条
  • [1] Electrostatic and non-electrostatic contributions to the binding free energies of anthracycline antibiotics to DNA
    Baginski, M
    Fogolari, F
    Briggs, JM
    [J]. JOURNAL OF MOLECULAR BIOLOGY, 1997, 274 (02) : 253 - 267
  • [2] Biomolecular applications of Poisson-Boltzmann methods
    Baker, NA
    [J]. REVIEWS IN COMPUTATIONAL CHEMISTRY, VOL 21, 2005, 21 : 349 - 379
  • [3] GFN2-xTB-An Accurate and Broadly Parametrized Self-Consistent Tight-Binding Quantum Chemical Method with Multipole Electrostatics and Density-Dependent Dispersion Contributions
    Bannwarth, Christoph
    Ehlert, Sebastian
    Grimme, Stefan
    [J]. JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 2019, 15 (03) : 1652 - 1671
  • [4] A WELL-BEHAVED ELECTROSTATIC POTENTIAL BASED METHOD USING CHARGE RESTRAINTS FOR DERIVING ATOMIC CHARGES - THE RESP MODEL
    BAYLY, CI
    CIEPLAK, P
    CORNELL, WD
    KOLLMAN, PA
    [J]. JOURNAL OF PHYSICAL CHEMISTRY, 1993, 97 (40) : 10269 - 10280
  • [5] Electrostatic Potential Derived Atomic Charges for Periodic Systems Using a Modified Error Functional
    Campana, Carlos
    Mussard, Bastien
    Woo, Tom K.
    [J]. JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 2009, 5 (10) : 2866 - 2878
  • [6] Cook D.B., 2005, HDB COMPUTATIONAL QU
  • [7] Molecular Engineering of Indoline-Based D-A-π-A Organic Sensitizers toward High Efficiency Performance from First-Principles Calculations
    Ding, Wei-Lu
    Wang, Dong-Mei
    Geng, Zhi-Yuan
    Zhao, Xiao-Ling
    Yan, Yun-Feng
    [J]. JOURNAL OF PHYSICAL CHEMISTRY C, 2013, 117 (34) : 17382 - 17398
  • [8] Computational methods for biomolecular electrostatics
    Dong, Feng
    Olsen, Brett
    Baker, Nathan A.
    [J]. BIOPHYSICAL TOOLS FOR BIOLOGISTS: VOL 1 IN VITRO TECHNIQUES, 2008, 84 : 843 - +
  • [9] A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations
    Duan, Y
    Wu, C
    Chowdhury, S
    Lee, MC
    Xiong, GM
    Zhang, W
    Yang, R
    Cieplak, P
    Luo, R
    Lee, T
    Caldwell, J
    Wang, JM
    Kollman, P
    [J]. JOURNAL OF COMPUTATIONAL CHEMISTRY, 2003, 24 (16) : 1999 - 2012
  • [10] A METHOD FOR 2-ELECTRON GAUSSIAN INTEGRAL AND INTEGRAL DERIVATIVE EVALUATION USING RECURRENCE RELATIONS
    HEADGORDON, M
    POPLE, JA
    [J]. JOURNAL OF CHEMICAL PHYSICS, 1988, 89 (09) : 5777 - 5786