Connecting Molecular Energy Landscape Analysis with Markov Model-based Analysis of Equilibrium Structural Dynamics

• DOI: 10.29007/tmgc
• Publication Date: 2019-03-18T23:10:39Z
• Authors: Kazi Lutful Kabir; Nasrin Akhter; Amarda Shehu
• Keywords: Energy landscape; Macro; Identification

Molecular dynamics simulation software now provides us with a view of the structure space accessed by molecule. Increasingly, Markov state models are proposed to integrate various simulations molecule and extract its equilibrium structural dynamics. The approach relies on organizing structures in into states as an at- tempt identify thermodynamically-stable semi-stable (macro)states among which transitions can then be quantified. Typically, off-the-shelf clustering algorithms used for this purpose. In paper, we investigate two additional complementary approaches identification that rely graph embeddings structures. particular, show doing so allows revealing basins energy landscape associated space. Moreover, demonstrate basins, directly tied stable states, yield better model proof-of-concept application.