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A QM-MM interface between CHARMM and TURBOMOLE: implementation and application to systems in bulk phase and
Markus J Loferer1, Hannes H Loeffler, Klaus R Liedl
1Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innrain 52a, A-6020 Innsbruck, Austria.
Journal of Computational Chemistry
|June 24, 2003
Summary
This study introduces a hybrid quantum mechanics/molecular mechanics (QM/MM) method linking TURBOMOLE and CHARMM. This approach efficiently combines parallel QM calculations with CHARMM
Area of Science:
- Computational Chemistry
- Biophysics
- Biochemistry
Background:
- Hybrid quantum mechanics/molecular mechanics (QM/MM) methods are crucial for studying complex molecular systems.
- Integrating ab initio and density functional theory (DFT) with molecular mechanics (MM) presents computational challenges.
- Efficiently utilizing computational resources for QM/MM simulations is an ongoing research area.
Purpose of the Study:
- To describe the implementation of a novel hybrid QM/MM approach combining TURBOMOLE and CHARMM.
- To enable data exchange between ab initio/DFT (TURBOMOLE) and MM (CHARMM) software.
- To leverage TURBOMOLE's parallel processing for QM calculations within CHARMM simulations.
Main Methods:
- Developed an interface for seamless data exchange between TURBOMOLE and CHARMM.
- Utilized TURBOMOLE's multiprocessor capabilities for quantum mechanical (QM) calculations.
- Employed CHARMM's modules (e.g., TRAVEL, VIBRAN) for molecular mechanics (MM) tasks and analysis.
- Investigated various QM/MM boundaries and computationally efficient methods like RI-J.
- Studied systems with large QM regions, including a cobalt-containing B(12) cofactor.
Main Results:
- The hybrid QM/MM methodology was successfully implemented and tested.
- Performance was satisfactory across different quantum mechanical methods (Hartree-Fock, DFT) and QM/MM boundaries.
- The RI-J method proved suitable for QM/MM applications.
- Transition metal systems and large QM regions were effectively studied.
- Saddle points for the Menshutkin reaction in the condensed phase were located and verified using CHARMM's TRAVEL module.
Conclusions:
- The developed QM/MM approach provides a robust and efficient framework for complex molecular simulations.
- The integration allows for the exploitation of parallel computing for demanding QM calculations.
- This method facilitates the study of challenging chemical reactions and systems, including those with transition metals.
- The successful application to the Menshutkin reaction demonstrates the utility of the approach for reaction mechanism studies.