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. Author manuscript; available in PMC: 2013 Mar 21.
Published in final edited form as: J Chem Theory Comput. 2012 Sep 27;8(12):5035–5051. doi: 10.1021/ct3006248

Fig. 3.

Fig. 3

Reaction pathways of alanine dipeptide isomerization using NEB method. In pathways 1~3, the elastic force constant k is 10, 100 and 1000 kcal•mol−1• Å−2, respectively. The mass-weighted RMSD of all the atoms is used to measure the distance between replicas. The pathways 4~6 repeat the calculations of 1~3 with hydrogens excluded from mass-weighted RMSD calculation.