Communication: On the locality of Hydrogen bond networks at hydrophobic interfaces

Lambeth, Bradley; Junghans, Christoph; Kremer, Kurt; Clementi, Cecilia; Site, Luigi Delle

doi:10.1063/1.3522773

Cited by 57 publications

(63 citation statements)

References 36 publications

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“…With the broad parameterization of the MARTINI model and available user-friendly tools, such as MARTINI insane [63] and CHARMM-GUI Martini Maker [64], the possible future applications appear numerous. For example, our dual-resolution model is able to provide additional physical insight into the extent of hydrogen bond network in the solvation shells of solute molecules [16,65]. In our case, the atomistic water is coupled to the charge neutral MARTINI water model that is non-polar.…”

Section: Discussionmentioning

confidence: 99%

Adaptive resolution simulation of an atomistic DNA molecule in MARTINI salt solution

Zavadlav

Podgornik

Melo

et al. 2016

Eur. Phys. J. Spec. Top.

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Abstract. We present a dual-resolution model of a deoxyribonucleic acid (DNA) molecule in a bathing solution, where we concurrently couple atomistic bundled water and ions with the coarse-grained MAR-TINI model of the solvent. We use our fine-grained salt solution model as a solvent in the inner shell surrounding the DNA molecule, whereas the solvent in the outer shell is modeled by the coarse-grained model. The solvent entities can exchange between the two domains and adapt their resolution accordingly. We critically asses the performance of our multiscale model in adaptive resolution simulations of an infinitely long DNA molecule, focusing on the structural characteristics of the solvent around DNA. Our analysis shows that the adaptive resolution scheme does not produce any noticeable artifacts in comparison to a reference system simulated in full detail. The effect of using a bundled-SPC model, required for multiscaling, compared to the standard free SPC model is also evaluated. Our multiscale approach opens the way for large scale applications of DNA and other biomolecules which require a large solvent reservoir to avoid boundary effects.

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Section: Discussionmentioning

confidence: 99%

Adaptive resolution simulation of an atomistic DNA molecule in MARTINI salt solution

Zavadlav

Podgornik

Melo

et al. 2016

Eur. Phys. J. Spec. Top.

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“…In the AdResS setup, on the other hand, finite-size effect can be neglected for sufficiently large boxes, thus allowing one to characterize the response of the system's properties in a small subregion when atomistic interactions with the bulk are switched off, but the thermodynamics is the same as in a fully-atomistic simulation. An example of this applications is provided by the work in Reference [175]: here a molecule with both hydrophilic and hydrophobic interactions was solvated in water and put at the center of the high-resolution region, while the water molecules far from the surface were treated at the coarse-grained level. The ordering degree of the hydrogen bond network on the molecule's surface was measured as a function of the size of the all-atom region: the results showed a dependency of the ordering for water molecules close to the surface of the repulsive solute, while no relevant effect was observed for the attractive case.…”

Section: Applicationsmentioning

confidence: 99%

Computer Simulations of Soft Matter: Linking the Scales

Potestio

Peter

Kremer

2014

Entropy

Self Cite

102

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Abstract:In the last few decades, computer simulations have become a fundamental tool in the field of soft matter science, allowing researchers to investigate the properties of a large variety of systems. Nonetheless, even the most powerful computational resources presently available are, in general, sufficient to simulate complex biomolecules only for a few nanoseconds. This limitation is often circumvented by using coarse-grained models, in which only a subset of the system's degrees of freedom is retained; for an effective and insightful use of these simplified models; however, an appropriate parametrization of the interactions is of fundamental importance. Additionally, in many cases the removal of fine-grained details in a specific, small region of the system would destroy relevant features; such cases can be treated using dual-resolution simulation methods, where a subregion of the system is described with high resolution, and a coarse-grained representation is employed in the rest of the simulation domain. In this review we discuss the basic notions of coarse-graining theory, presenting the most common methodologies employed to build low-resolution descriptions of a system and putting particular emphasis on their similarities and differences. The AdResS and H-AdResS adaptive resolution simulation schemes are reported as examples of dual-resolution approaches, especially focusing in particular on their theoretical background.

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“…Despite its conceptual simplicity, this approach produced highly satisfactory results for a large variety of systems and physical situations [31][32][33][34][35][36][37][38]. However, exactly because it turned to be a numerically satisfactory approach, a deeper conceptual justification of the idea was mandatory.…”

Section: Gc-adress: Basicsmentioning

confidence: 99%

Grand Canonical adaptive resolution simulation for molecules with electrons: A theoretical framework based on physical consistency

Site

2018

Computer Physics Communications

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A theoretical scheme for the treatment of an open molecular system with electrons and nuclei is proposed. The idea is based on the Grand Canonical description of a quantum region embedded in a classical reservoir of molecules. Electronic properties of the quantum region are calculated at constant electronic chemical potential equal to that of the corresponding (large) bulk system treated at full quantum level. Instead, the exchange of molecules between the quantum region and the classical environment occurs at the chemical potential of the macroscopic thermodynamic conditions. T he Grand Canonical Adaptive Resolution Scheme is proposed for the treatment of the classical environment; such an approach can treat the exchange of molecules according to first principles of statistical mechanics and thermodynamic. The overall scheme is build on the basis of physical consistency, with the corresponding definition of numerical criteria of control of the approximations implied by the coupling. Given the wide range of expertise required, this work has the intention of providing guiding principles for the construction of a well founded computational protocol for actual multiscale simulations from the electronic to the mesoscopic scale.

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Communication: On the locality of Hydrogen bond networks at hydrophobic interfaces

Cited by 57 publications

References 36 publications

Adaptive resolution simulation of an atomistic DNA molecule in MARTINI salt solution

Adaptive resolution simulation of an atomistic DNA molecule in MARTINI salt solution

Computer Simulations of Soft Matter: Linking the Scales

Grand Canonical adaptive resolution simulation for molecules with electrons: A theoretical framework based on physical consistency

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