[2P-33] Benchmarking the free energy calculation of PaCS-MD/MSM
Parallel Cascade Selection Molecular Dynamics simulations with the Markov State Model (PaCS-MD/MSM) has been reported to be an efficient method to calculate the binding free energy of given protein complexes. Here we massively perform binding free energy calculation of Adenosine A2a receptor with a variety of agonists and antagonist, heat shock protein HSP90 with inhibitors. These ligands are selected because they are strong binders. We perform 5 trial for each complex and number of replicas is set to be 30 in PaCS-MD. The obtained results again emphasize the performance of the method.