Adaptive Resolution Simulation of a DNA Molecule in Salt Solution

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• 作者：Julija Zavadlav ; Rudolf Podgornik ; Matej Praprotnik
• 刊名：Journal of Chemical Theory and Computation
• 出版年：2015
• 出版时间：October 13, 2015
• 年：2015
• 卷：11
• 期：10
• 页码：5035-5044
• 全文大小：713K
• ISSN：1549-9626

文摘

We present a multiscale simulation of a DNA molecule in 1 M NaCl salt solution environment, employing the adaptive resolution simulation approach that allows the solvent molecules, i.e., water and ions, to change their resolution from atomistic to coarse-grained and vice versa adaptively on-the-fly. The region of high resolution moves together with the DNA center-of-mass so that the DNA itself is always modeled at high resolution. We show that our multiscale simulations yield a stable DNA鈥搒olution system, with statistical properties similar to those produced by the conventional all-atom molecular dynamics simulation. Special attention is given to the collective properties, such as the dielectric constant, as they provide a sensitive quality measure of our multiscale approach.