2019
DOI: 10.1103/physrevresearch.1.033099
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Investigation of the hydration shell of a membrane in an open system molecular dynamics simulation

Abstract: We analyze structural properties of hydration for a biological membrane with the open boundary adaptive resolution molecular dynamics approach in its latest version. A large region of noninteracting pointlike particles (tracers) acts as a reservoir of molecules and energy for the atomistically resolved membrane-water interface. The drastic simplification of the environment and its simple coupling to the high-resolution region has been successfully tested in a previous work on pure liquid water, and this work r… Show more

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Cited by 17 publications
(17 citation statements)
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“…The AdResS analysis, by identifying the minimal AT region, of about 0.7nm from the surface of the membrane, within which the membrane has a direct effect on the structural properties of water (and vice versa), reproduces results of a reference full atomistic simulation and of recent experiments (see the detailed discussion in Ref. [77]).…”
Section: Study Of the Hydration Shell Of A Membrane With The Open System Protocol Of Adresssupporting
confidence: 59%
See 1 more Smart Citation
“…The AdResS analysis, by identifying the minimal AT region, of about 0.7nm from the surface of the membrane, within which the membrane has a direct effect on the structural properties of water (and vice versa), reproduces results of a reference full atomistic simulation and of recent experiments (see the detailed discussion in Ref. [77]).…”
Section: Study Of the Hydration Shell Of A Membrane With The Open System Protocol Of Adresssupporting
confidence: 59%
“…In Ref. [77] the AdResS approach with tracers has been applied to the hydration of a DPPC bilayer. The atomistic system of reference consists of a bilayer of 180 (90 per leaflet) DPPC molecules, solvated with 52470 water molecules (see Fig.…”
Section: Study Of the Hydration Shell Of A Membrane With The Open System Protocol Of Adressmentioning
confidence: 99%
“…[ 175 ] Finally, an even more drastic simplification of the model of Krekeler et al., [ 183 ] in closer connection to the idea of open system embedded in a generic thermodynamic reservoir was pursued recently. [ 123,184 ] Here, the CG region is substituted by a reservoir of non‐interacting point‐particle (tracers). The AT region exchanges particles and energy with the reservoir in an adaptive manner as in the standard AdResS (see panel (c) of Figure 1).…”
Section: Adress and Open Systems Modelsmentioning
confidence: 99%
“…The abrupt coupling approach allows for efficient simulations of complex systems such as, for example, hydrated biological membranes. [16] While the standard atomistic simulation would require a sizable computational effort, the AdResS simulation, due to the drastically reduced number of degrees of freedom, runs at a reduced computational cost. It must be noticed that the initial calibration and validation of In panel (c) it is shown the x-direction along which the change of resolution occurs and the vector n, normal to the coupling boundaries, that defines the direction of the thermodynamic force.…”
Section: Introductionmentioning
confidence: 99%
“…The computational cost of such test systems, even at fully atomistic level, is negligible (see e.g., refs. [16][17][18]).…”
Section: Introductionmentioning
confidence: 99%