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. Author manuscript; available in PMC: 2021 May 12.
Published in final edited form as: J Chem Theory Comput. 2020 Apr 27;16(5):3221–3239. doi: 10.1021/acs.jctc.0c00057

Figure 4.

Figure 4.

RMSD analyses based on the Cα atoms for a) protein GB3 system (PDB: 2IGD) and b) HP7 peptide (PDB: 2EVQ), using the original Drude-2013 protein FF (Drude-2013, in black), Drude-2013 with optimized backbone parameters only (Drude-2013-opt-backbone, in green), and final optimized Drude-2019 protein FF (Drude-2019, in blue). Structures obtained at the end of the simulations are shown in cyan, indicated with the corresponding colored arrows.