Journal Article

FZJ-2017-07069

http://join2-wiki.gsi.de/foswiki/pub/Main/Artwork/join2_logo100x88.png Open Boundary Simulations of Proteins and Their Hydration Shells by Hamiltonian Adaptive Resolution Scheme

Tarenzi, T. ; Calandrini, V. (Corresponding author)FZJ* ; Potestio, R. ; Giorgetti, A.FZJ* ; Carloni, P.FZJ*

2017
Washington, DC

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Please use a persistent id in citations: http://hdl.handle.net/2128/16225  doi:10.1021/acs.jctc.7b00508

Abstract: The recently proposed Hamiltonian Adaptive Resolution Scheme (H-AdResS) allows to perform molecular simulations in an open boundary framework. It allows to change on the fly the resolution of specific subset of molecules (usually the solvent), which are free to diffuse between the atomistic region and the coarse-grained reservoir. So far, the method has been successfully applied to pure liquids. Coupling the H-AdResS methodology to hybrid models of proteins, such as the Molecular Mechanics/Coarse-Grained (MM/CG) scheme, is a promising approach for rigorous calculations of ligand binding free energies in low-resolution protein models. Towards this goal, here we apply for the first time H-AdResS to two atomistic proteins in dual-resolution solvent, proving its ability to reproduce structural and dynamic properties of both the proteins and the solvent, as obtained from atomistic simulations.

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Contributing Institute(s):

1. Computational Biomedicine (IAS-5)
2. Computational Biomedicine (INM-9)

Research Program(s):

1. 574 - Theory, modelling and simulation (POF3-574) (POF3-574)

Appears in the scientific report 2017

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Database coverage:
; ; Current Contents - Physical, Chemical and Earth Sciences ; Free to read ; IF >= 5 ; JCR ; SCOPUS ; Science Citation Index ; Science Citation Index Expanded ; Thomson Reuters Master Journal List ; Web of Science Core Collection

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