Replica exchange molecular dynamics study of short helical peptide critical role played by electrost

• 作 者: Ya Gao Xiaoliang Lu John Z.H.Zhang Ye Mei
• 机 构: StateKeyLaboratoryofPrecisionSpectroscopy,EastChinaNormalUniversity,Shanghai200062,ChinaStateKeyLabo
• 出 处: 第六届国际理论化学、分子模拟和生命科学研讨会暨科学计算和模拟软件发展平台学术交流会
• 发表日期: 2011年11期

　　Folding simulations often get biased by flaws in force field employed.In this work, we propose a novel formula based atomic charge polarization model to surmount the homogeneous approximation in traditional AMBER force field.With this charge model, we study the folding of a short helical peptide 2I9M using replica exchange molecular dynamics, and compare the result with AMBER03 charge.In AMBER03 simulation, we find a decoy structure which has nearly the same free energy as the folded structure, which makes the simulation less reliable.