ISSN:
1432-2234
Keywords:
Key words: Macromolecular systems
;
Molecular dynamics
;
Quantum mechanics
;
Molecular mechanics
;
Frequencies
Source:
Springer Online Journal Archives 1860-2000
Topics:
Chemistry and Pharmacology
Notes:
Abstract. A technique for implementing the integrated molecular orbital and molecular mechanics (IMOMM) methodology developed by Maseras and Morokuma that is used to perform combined quantum mechanics/molecular mechanics (QM/MM) molecular dynamics simulations, frequency calculations and simulations of macromolecules including explicit solvent is presented. Although the IMOMM methodology is generalized to any coordinate system, the implementation first described by Maseras and Morokuma requires that the QM and MM gradients be transformed into internal coordinates before they are added together. This coordinate transformation can be cumbersome for macromolecular systems and can become ill-defined during the course of a molecular dynamics simulation. We describe an implementation of the IMOMM method in which the QM and MM gradients are combined in the cartesian coordinate system, thereby avoiding potential problems associated with using the internal coordinate system. The implementation can be used to perform combined QM/MM molecular dynamics simulations and frequency calculations within the IMOMM framework. Finally, we have examined the applicability of thermochemical data derived from IMOMM framework. Finally, we have examined the applicability of thermochemical data derived from IMOMM frequency calculations.
Type of Medium:
Electronic Resource
URL:
http://dx.doi.org/10.1007/s002140050391
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