To understand molecular functions from long time molecular dyn amics simulations, we developed perturbation analyses of atomic interactions based on maximization of the Kullback-Leibler divergence. Within the second order approximation of the divergence, we obtained following results:
(i) Perturbation analysis of intramolecular interactions can be solved by the principal component analysis (PCA) using intramolecular potential energy terms (Koyama et al., Phys. Rev. E 78, 046702 (2008)). (ii) Perturbation analysis of intermolecular interactions can be solved by the PCA using conditional expectations of the intermolecular potential energy terms (Koyama et al., submitted). (iii) Perturbation analysis of intermolecular interactions with distance dependency can be solved by the functional PCA using force times conditional cumulative density (Koyama et al., in preparation).