Action-derived molecular dynamics method for the simulation of rare events : from algorithms to applications

In-Ho Lee

Korea Research Institute of Standards and Science, 1 Doryong-dong, Yusong-gu, Daejon 305-600, Korea

We introduce a powerful method (action-derived molecular dynamics method) for exploring the transition pathways in rare events. Practical implementation of the algorithm requires the evaluation of the potential energy and the resulting atomic forces as in ordinary molecular-dynamics simulations. We illustrate this approach by conducting transition-pathway search simulations on a set of molecular systems, demonstrating its superiority over traditional approaches in sampling potential energy surfaces. Our applications include the formation pathways of C₆₀, C₆₀ fusion pathways, autocatalytic structural transformations of fullerenes, alanine dipeptide isomerization pathways, and folding pathways of an α-helix (acetyl-(Ala)₁₀-N-methyl amide) and a β-hairpin (residues 41-56 of protein G).