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. Author manuscript; available in PMC: 2023 Mar 8.
Published in final edited form as: J Chem Theory Comput. 2022 Feb 11;18(3):1359–1381. doi: 10.1021/acs.jctc.1c00590

Figure 7:

Figure 7:

Calculated electron densities (blue) from simulations compared to the experimental densities (white) of the thrombin system (PDB: 2ZFF). The target site is labeled. We only show the simulation block when we first observe a good agreement between the calculated and experimental density. Both grand and MD simulations can reproduce the experimental electron densities for the target site. Panel A and B are results from grand and MD simulations, respectively. The left and right columns are results from two replicates for each simulation technique. The number of force evaluations for one simulation block in replicate 1 in panel B is 35 million. The number of force evaluations for one simulation block in other panels is 1.4 million.