The behavior of collagen-like molecules in response to different temperature setting methods in steered molecular dynamic simulation

• Published in: 한국정보전자통신기술학회 논문지 Vol. 13; no. 5; pp. 397 - 402
• Main Authors: Young-June Yoon(윤영준), Kang-Hee Cho(조강희), Seog-Young Han(한석영)
• Format: Journal Article
• Language: English
• Published: 한국정보전자통신기술학회 01.10.2020
• Subjects: 전자/정보통신공학; collagen; stress-strain curve; constant temperature; molecular dynamics; viscoelasticity
• ISSN: 2005-081X; 2288-9302

Collagen type I is the most abundant protein in the human body. It shows viscoelastic behavior, which is what confers tendons with their viscoelastic properties. There are two different temperature setting methods in molecular dynamics simulations, namely rescaling and reassignment. The rescaling method maintains the temperature by scaling the given temperature, while the reassignment method sets the temperature according to a Maxwell distribution at the target temperature. We observed time-dependent behavior when the reassignment method was applied in tensile simulation, but not when the rescaling method was applied. Time-dependent behavior was observed only when the reassignment method was applied or when one side of the collagen molecule was stretched to a greater extent than the other side. As result, the collagen is elongated to 80nm, 100nm, 130nm, and 180nm, respectively, when the collagen is pulled by different velocities, 0.5, 1, 2, and 5 Å/ps, up to 40 Å. The results do not provide a detailed physical explanation, but the phenomena illustrated in this result are important for caution when further simulations are performed. KCI Citation Count: 0