Computational investigation of pLGICs interacting with general anesthetics is surprisingly tricky.  This article/chapter provides guidelines for reproducing the approach that we’ve refined over a decade.  Sruthi gives some warnings for avoiding docking pitfalls and tips on running unbiased (traditional) molecular dynamics simulation. For more advanced users, she provides steps for rigorously calculating binding affinities and testing convergence.

Physical Accuracy Leads to Biological Relevance: Best Practices For Simulation Ligand-Gated Ion Channels Interacting With General Anesthetics