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. Author manuscript; available in PMC: 2018 Sep 12.
Published in final edited form as: J Chem Theory Comput. 2017 Aug 31;13(9):4593–4603. doi: 10.1021/acs.jctc.7b00690

Figure 4.

Figure 4

(A) Top, Adaptive Levenberg-Marquardt (LM) algorithm matching 4 CVs: cleft distance, twist angle, and their second moments is compared to harmonic bias on angle and distance with large spring constants on both. Data is for all-atom MD simulations of the G/monomer system in Figure 1. Bottom, in blue, the LM algorithm is performed on an actin monomer starting from a filament structure (F/monomer in Figure 1). In red, the bias parameters at time 80 ns are fixed and a separate simulation is run using this learned bias. (B) Comparison of the structure of the G/monomer in the LM trajectory from (A,top) with a filament subunit by backbone RMSD. Color shows progress along the trajectory in (A).