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Thus, the total production MD length was 278 ns. In total, three independent folding events were observed in three different replicas. 7 ns. This suggests that MUCAREM can accelerate G-peptide folding more than 60 times than the conventional MD simulations, because the experimental folding time of G-peptide is 6 s [45]. 6 shows the time series of the heavy-atom Root Mean Square Deviation (RMSD) from the native configuration (coordinates in the PDB entry 2GB1) and representative snapshot structures observed in the folding events are shown for two replicas.

10 Implied Timescales and Number of Macrostates With the microstates generated from the first stage of clustering, we can construct the TPM based on the transitions between these states. Then if we attempt to do eigenvector decomposition of the TPM: Xi P . -T. Da et al. where each eigenvector Xi actually corresponds to a certain state distribution that can give rise to a sustainable mode of transitions between groups of states, with the signed structure of the eigenvector indicating the two groups between which the transition occurs.

Biopolymers 29:1–11 35. Wang J, Cieplak P, Kollman PA (2000) How well does a restrained electrostatic potential (RESP) model perform in calculating conformational energies of organic and biological molecules. J Comput Chem 21:1049–1074 36. Yoda T, Sugita Y, Okamoto Y (2004) Comparisons of force fields for proteins by generalizedensemble simulations. Chem Phys Lett 386:460–467 37. Yoda T, Sugita Y, Okamoto Y (2004) Secondary-structure preferences of force fields for proteins evaluated by generalized-ensemble simulations.

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Quantum Effects in Unimolecular Reaction Dynamics [thesis]

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