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. Author manuscript; available in PMC: 2010 Aug 1.
Published in final edited form as: J Comput Chem. 2009 Aug;30(11):1701–1711. doi: 10.1002/jcc.21268

Figure 6.

Figure 6

The running average of relative free energy changes in trypsin-ligand complex from explicit water MD simulations of ligand B and E. In both cases, the ligand is being perturbed into benzamidine.