In this paper, we introduce the Flexible Topology method and assess its performance on small ligand-only systems, determining suitable algorithmic parameters to help pave the way for more complex applications of the method, such as virtual screening. We first describe the mathematical framework of Flexible Topology and explain its implementation in the OpenMM molecular dynamics package. We define atomic environment vectors (AEVs) using functions from Behler and Parrinello that are used to both 1) map (or "assign") ghost particles to atoms of the target ligand and 2) define the loss function that guides the ghost particles toward the target structures. We find that for small ligands (20 atoms or less), this loss function is sufficient to reliably guide assembly of the target ligand. For larger ligands, additional "second-order" restraints that bring together specific pairs of atoms are useful to guide assembly. To thoroughly assess performance of the algorithm and determine suitable parameters, we run assembly simulations with a set of 10 target ligands in vacuum and define an appropriate metric for the quality of assembly. Finally, we conclude with a discussion of the challenges and future work of the Flexible Topology method, looking toward applications such as the prediction of bound poses, calculation of relative binding free energies, and fast virtual screening of large ligand sets.