 relative binding free energy of about +0.5 kcal/mol. </p>
<p>
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<h3>Single-topology simulation</h3>
The calculation above is dual-topology, which means that the two ligands are simulated simultaneously. There is an alternative methodology that is called single-topology where only a single ligand is simulated but the force field of this ligand is perturbed. This methodology has some advantages when the difference between the two ligand is small such as in our case. Therefore, we will