Adaptive resolution simulation of an atomistic protein in MARTINI water
نویسندگان
چکیده
منابع مشابه
Adaptive resolution simulation of an atomistic protein in MARTINI water.
We present an adaptive resolution simulation of protein G in multiscale water. We couple atomistic water around the protein with mesoscopic water, where four water molecules are represented with one coarse-grained bead, farther away. We circumvent the difficulties that arise from coupling to the coarse-grained model via a 4-to-1 molecule coarse-grain mapping by using bundled water models, i.e.,...
متن کاملSupporting Information for Adaptive resolution simulation of MARTINI solvents
The Langevin thermostat does not reproduce the correct hydrodynamics, i.e., the hydrodynamic interactions are unphysically screened. To correctly describe hydrodynamic interactions, we have to use the DPD thermostat1,2 instead. The DPD thermostat satisfies Newton’s third law by construction and owing to mass, momentum and temperature conservation, hydrodynamics is also properly reproduced.3 We ...
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Multiscale methods are the most efficient way to address the interlinked spatiotemporal scales encountered in soft matter and molecular liquids. In the literature reported hybrid approaches span from quantum to atomistic, coarse-grained, and continuum length scales. In this article, we present the hybrid coupling of the molecular dynamics (MD) and dissipative particle dynamics (DPD) methods, br...
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We present a dual-resolution molecular dynamics (MD) simulation of liquid water employing a recently introduced Adaptive Resolution Scheme (AdResS). The spatially adaptive molecular resolution procedure allows for changing from a coarse-grained to an all-atom representation and vice versa on-the-fly. In order to find the most appropriate coarse-grained water model to be employed with AdResS, we...
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A Monte Carlo simulation study of water and hydrocarbons aiming at understanding the degradation of polyethylene cable insulation is presented. Atomistic simulations of water, hydrocarbons and ions are presented. The SPC/E and TraPPE potential functions are used. The equilibrium distributions and clustering of water in vapour and in hydrocarbons was investigated using Gibbs-ensemble Monte-Carlo...
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ژورنال
عنوان ژورنال: The Journal of Chemical Physics
سال: 2014
ISSN: 0021-9606,1089-7690
DOI: 10.1063/1.4863329