Probing the energy landscape of alanine dipeptide and decalanine using temperature as a tunable parameter in molecular dynamics

[摘要] We perform several molecular dynamics (MD) calculations of solvated alanine dipeptide and decalanine in vacuum with temperature as a tunable parameter and in the process, generate Markov state models (MSMs) at each temperature. An interesting observation that the kinetic rates appear to obey the Arrhenius rate law allows us to predict the dynamics of alanine dipeptide at 300 K at the microsecond timescales using the nanoseconds long high temperature calculations without actually performing MD simulations at 300 K. We conclude that the energy landscape of alanine dipeptide contains superbasins deeper than kBT and determine the energy barriers associated with the moves from the Arrhenius rate expression. Similar insights regarding the energy landscape associated with folding/unfolding pathways of a deca-alanine molecule are obtained using kinetic rates calculated at different temperatures.

[发布机构] Department of Physics, Indian Institute of Technology Guwahati, Guwahati; Assam; 781039, India^1;Department of Chemical Engineering, Indian Institute of Technology, Maharashtra Bombay, India^2

[效力级别] 计算机科学 [学科分类] 计算机科学（综合）

[关键词] Alanine dipeptides;Arrhenius Rate Law;Energy landscape;High temperature;Kinetic rates;Markov State models;Rate expression;Tunable parameter