Merging Topologies for Relative Binding Free Energies
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| Zeke A. Piskulich\ :sup:`1`,  Patricio Barletta\ :sup:`1`, Ryan Snyder\ :sup:`1`, and Darrin M. York\ :sup:`1`
| :sup:`1`\ Laboratory for Biomolecular Simulation Research, Institute
|   for Quantitative Biomedicine and Department of Chemistry and Chemical
|   Biology, Rutgers University, Piscataway, NJ 08854, USA

Learning objectives
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- Learn how to merge topologies for Relative Binding Free Energy simulations

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Activity
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.. start-tutorial

Merging Topologies
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One of the most challenging stages for setting up an RBFE calculation by hand is to generate merged topologies for each endstate. Though at a particular end-state one ligand is fully turned off, both ligands must be present so that they can share a common core. 



.. end-tutorial