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The intra-molecular potential was parameterized to simulate a rigid structure with surface hydroxyl groups that are free to rotate in an AMBER-style torsional potential.
These details may reflect imperfections of the force field, which is not parameterized to account for ligand to metal charge transfer and polarization effects.
The models differ from previous approaches in that they are parameterized directly in terms of selection coefficients.
Although we could have parameterized anions based on solvation data alone, the effort here is to isolate the role of size and to maintain as straightforward an analysis as possible.
The method was parameterized with the aim of retrieving the native structure of bacteriorhodopsin among near- and far-from-native templates.
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