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복잡계 자기조립 연구단
복잡계 자기조립 연구단
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Simple method for Hybrid All-Atom and Coarse-Grained Molecular Dynamics Simulations and Its Applications

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Title
Simple method for Hybrid All-Atom and Coarse-Grained Molecular Dynamics Simulations and Its Applications
Author(s)
Sun Mi Choi; Pandian Sokkar; Young Min Rhee
Publication Date
2014-01
Journal
BIOPHYSICAL JOURNAL, v.106, no.2, pp.413A - 413A
Publisher
CELL PRESS
Abstract
Hybrid all-atom (AA) and coarse-grained (CG) simulation has the possibility of overcoming the limitations of both AA and CG molecular dynamics (MD) simulations. HybridAA/CGsystems are practicable to simulatemicrosecond timescale and to get detailed information formolecular structures.Many existingmethods for hybrid AA/CG simulations tend to require heavy parameterizations that complicate multiscale simulations. We test a simple scheme for simulating hybrid AA/ CG systems using standard AA and CG force fields, together with four small proteins as test cases for the scheme.Our method uses virtual sites for interactions betweenCGandAAresolution as reported earlier (Rzepiela et al.Phys.Chem.Chem. Phys. 2011, 13, 10437-10448) and we add distance restrained FG water layer to improve the reliability of the hybrid simulation. We observe that the addition of distance restrained FG water layer in the hybrid simulation results in close accord with the structure from the atomistic simulations. However, there are also digressions fromcorrect behaviors that need to be addressed in future developments.We show such various results in detail and discuss the prospects of our scheme.
URI
https://pr.ibs.re.kr/handle/8788114/799
ISSN
0006-3495
Appears in Collections:
Center for Self-assembly and Complexity(복잡계 자기조립 연구단) > Journal Papers (저널논문)
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