Evaluating Boundary Dependent Errors in QM/MM Simulations

SOLT, Ivan, Petr KULHÁNEK, Istvan SIMON, Steven WINFIELD, Mike C PAYNE, Gabor CSANYI a Monika FUXREITER. Evaluating Boundary Dependent Errors in QM/MM Simulations. Journal of Physical Chemistry B. New York: American Chemical Society, 2009, roč. 2009, 113(17), s. 5728-5735, 7 s. ISSN 1520-6106.

Základní údaje

• Originální název: Evaluating Boundary Dependent Errors in QM/MM Simulations
• Autoři: SOLT, Ivan, Petr KULHÁNEK, Istvan SIMON, Steven WINFIELD, Mike C PAYNE, Gabor CSANYI a Monika FUXREITER.
• Vydání: Journal of Physical Chemistry B, New York, American Chemical Society, 2009, 1520-6106.

Další údaje

• Originální jazyk: angličtina
• Typ výsledku: Článek v odborném periodiku
• Obor: 10402 Inorganic and nuclear chemistry
• Stát vydavatele: Spojené státy
• Utajení: není předmětem státního či obchodního tajemství
• Impakt faktor: Impact factor: 3.471
• Organizační jednotka: Přírodovědecká fakulta
• UT WoS: 000265529900009
• Klíčová slova anglicky: hybrid quantum mechanics/molecular mechanics; force error
• Příznaky: Recenzováno

Anotace

Hybrid quantum mechanics/molecular mechanics (QM/MM) simulations provide a powerful tool for studying chemical reactions, especially in complex biochemical systems. In most works to date, the quantum region is kept fixed throughout the simulation and is defined in an ad hoc way based on chemical intuition and available computational resources. The simulation errors associated with a given choice of the quantum region are, however, rarely assessed in a systematic manner. Here we study the dependence of two relevant quantities on the QM region size: the force error at the center of the QM region and the free energy of a proton transfer reaction. Taking lysozyme as our model system, we find that in an apolar region the average force error rapidly decreases with increasing QM region size. In contrast, the average force error at the polar active site is considerably higher, exhibits large oscillations and decreases more slowly, and may not fall below acceptable limits even for a quantum region radius of 9.0 angstrom. Although computation of free energies could only be afforded until 6.0 angstrom, results were found to change considerably within these limits. These errors demonstrate that the results of QM/MM calculations are heavily affected by the definition of the QM region (not only its size), and a convergence test is proposed to be a part of setting up QM/MM simulations.