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Multiple starting geometries were used to enhance the amount of conformational sampling, which has been found to be important in other enzyme studies.
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The resulting geometries served to generate the different starting geometries needed for computing the mechanism for nitrate reduction.
The starting geometries for the substrate and product complexes are generated by slight distortion of M O and O NO2 in the optimized transition state geometries, 6a and 6b.
Large-scale classical simulations may be essential in establishing starting geometries for subsequent QM/MM calculations.
Although changes in the relative orientation of the participating atoms and molecules in models M1 M6 were modest, small changes in the starting geometries resulted in significantly different geometries in M7.
Simplified meshes are also useful to export for use as starting geometry for simulation models.
Fourthly, we used multiple starting points, which means that the computations started with different initial values.
If multiple local maxima are suspected, then multiple trials using multiple starting places will help to identify them.
Prepare multiple fire starting options.
Gas phase geometries optimized using X-ray crystallography geometries as start geometries were found to be close to the start geometries.
Figure 9 Molecular start geometry.
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