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The CHARMM-TURBOMOLE interface for efficient and accurate QM/MM molecular dynamics, free energies, and excited state properties
| Content Provider | Semantic Scholar |
|---|---|
| Author | Riahi, Saleh Rowley, Christopher N. |
| Copyright Year | 2014 |
| Abstract | The quantum mechanical (QM)/molecular mechanical (MM) interface between Chemistry at HARvard Molecular Mechanics (CHARMM) and TURBOMOLE is described. CHARMM provides an extensive set of simulation algorithms, like molecular dynamics (MD) and free energy perturbation, and support for mature nonpolarizable and Drude polarizable force fields. TURBOMOLE provides fast QM calculations using density functional theory or wave function methods and excited state properties. CHARMM-TURBOMOLE is well-suited for extended QM/MM MD simulations using first principles methods with large (triple-ζ) basis sets. We demonstrate these capabilities with a QM/MM simulation of Mg(2+) (aq), where the MM outer sphere water molecules are represented using the SWM4-NDP Drude polarizable force field and the ion and inner coordination sphere are represented using QM PBE, PBE0, and MP2 methods. The relative solvation free energies of Mg(2+) and Zn(2+) were calculated using thermodynamic integration. We also demonstrate the features for excited state properties. We calculate the time-averaged solution absorption spectrum of indole, the emission spectrum of the indole 1La excited state, and the electronic circular dichroism spectrum of an oxacepham. |
| Starting Page | 67626 |
| Ending Page | 67638 |
| Page Count | 13 |
| File Format | PDF HTM / HTML |
| Alternate Webpage(s) | http://www.chem.mun.ca/homes/cnrhome/group_page/charmm-turbomole.pdf |
| Alternate Webpage(s) | https://www.wikidata.org/entity/Q51045211 |
| PubMed reference number | 25178266v1 |
| Alternate Webpage(s) | https://doi.org/10.1002/jcc.23716 |
| DOI | 10.1002/jcc.23716 |
| Journal | Journal of Computational Chemistry |
| Volume Number | 35 |
| Issue Number | 28 |
| Language | English |
| Access Restriction | Open |
| Subject Keyword | Algorithm Analysis of algorithms Anatomy, Regional Basis set (chemistry) CHARMM Circular dichroism Computer simulation Density functional theory Distance Dual Energy Citations Database Energy, Physics Excitation Excited state Force field (chemistry) Free energy perturbation Functional theories of grammar Interface Device Component Ions Mechanical ventilation Molecular dynamics Molecular mechanics Møller–Plesset perturbation theory Oscillator Device Component QM/MM Quantum mechanics Radial (radio) Semantics (computer science) Simulation THANATOPHORIC DYSPLASIA, TYPE I (disorder) TURBOMOLE Thermodynamic integration Thermodynamics Vibration - physical agent acetonitrile kilocalorie micacocidin A zinc cation |
| Content Type | Text |
| Resource Type | Article |
