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However, if conformers that make good hydrogen bonds to ionized sites are unavailable, the calculated ionization free energy will be wrong.
Here we present a new method to carry out the sampling, and to identify low energy conformers of the molecule.
Water gets conformers to make and accept available hydrogen bonds plus a conformer with no interaction with the protein, representing water in bulk solvent.
Occasionally during the simulated time some of the hydrogen bonds characteristic of the starting conformer were broken and hydrogen bonds typical of other conformers were formed for short time intervals.
The criteria for defining a conformer were based solely upon the type of intramolecular hydrogen bonds that characterized the analyzed conformations irrespective of other geometrical parameters.
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