Molecular dynamics studies of solvated polypeptides: Why the cut-off scheme does not work

Schreiber, Hellfried; Steinhauser, Othmar

doi:10.1016/0301-0104(92)80111-8

Cited by 117 publications

(76 citation statements)

References 30 publications

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“…The importance of accurately accounting for long-range interactions in molecular dynamics simulations has been an area of active research for a long time as it is a crucial issue in computational modeling [59,60,[62][63][64][65][66][67][68][69][70]. It is essential there-fore, to develop reliable and efficient methods to deal with these interactions as well as to use them with care and insight.…”

Section: Molecular Dynamic Simulations Of Ion Channelsmentioning

confidence: 99%

Molecular dynamics simulations of potassium channels

Domene

2007

Open Chemistry

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Despite the complexity of ion-channels, MD simulations based on realistic all-atom models have become a powerful technique for providing accurate descriptions of the structure and dynamics of these systems, complementing and reinforcing experimental work. Successful multidisciplinary collaborations, progress in the experimental determination of three-dimensional structures of membrane proteins together with new algorithms for molecular simulations and the increasing speed and availability of supercomputers, have made possible a considerable progress in this area of biophysics. This review aims at highlighting some of the work in the area of potassium channels and molecular dynamics simulations where numerous fundamental questions about the structure, function, folding and dynamics of these systems remain as yet unresolved challenges.

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Section: Molecular Dynamic Simulations Of Ion Channelsmentioning

confidence: 99%

Molecular dynamics simulations of potassium channels

Domene

2007

Open Chemistry

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“…A lot of cutoff methods applied to the Coulombic interaction offer insufficient accuracy [21][22][23][24][25][26][27][28][29][30][31], and all of the results are highly sensitive to the cutoff distance. Cutoff methods are also applied to macromolecular systems [12][13][14][32][33][34][35][36][37][38][39][40][41][42][43], and many results indicate that the aforementioned approximations have difficulties when estimating these systems. On the other hand, advanced cutoff-like methods have been developed to avoid the aforementioned difficulties and to accelerate long-range interaction calculations.…”

Section: Introductionmentioning

confidence: 99%

Truncation Effects of Shift Function Methods in Bulk Water Systems

Takahashi

2013

Entropy

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A reduction of the cost for long-range interaction calculation is essential for large-scale molecular systems that contain a lot of point charges. Cutoff methods are often used to reduce the cost of long-range interaction calculations. Molecular dynamics (MD) simulations can be accelerated by using cutoff methods; however, simple truncation or approximation of long-range interactions often offers serious defects for various systems. For example, thermodynamical properties of polar molecular systems are strongly affected by the treatment of the Coulombic interactions and may lead to unphysical results. To assess the truncation effect of some cutoff methods that are categorized as the shift function method, MD simulations for bulk water systems were performed. The results reflect two main factors, i.e., the treatment of cutoff boundary conditions and the presence/absence of the theoretical background for the long-range approximation.

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“…Cutoff methods, however, are generally not recommended for use for the calculation of long-range electrostatic effects because of the risk of introducing substantial nonphysical effects [3][4][5][6] which result from both the abrupt termination of pairwise interactions in the vicinity of the cutoff and the neglect of longer-range electrostatic interactions. While calculation schemes that use smoothing functions have been shown to significantly reduce the presence of nonphysical effects due to the use of abrupt cutoffs, 7 the neglect of long-range interactions is still a serious concern.…”

Section: Introductionmentioning

confidence: 99%

Development of molecular simulation methods to accurately represent protein-surface interactions: Method assessment for the calculation of electrostatic effects

et al. 2009

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The simulation of the interactions of proteins with charged surfaces in a condensed-phase aqueous solution containing electrolytes using empirical force field based methods is predominantly governed by nonbonded interactions between the atoms of the protein, surface, and the solvent. Electrostatic effects represent the strongest type of these interactions and the type that is most difficult to accurately represent because of their long-range influence. While many different methods have been developed to represent electrostatic interactions, the particle mesh Ewald summation (PME) method is generally considered to be the most accurate one for calculating these effects. However, the PME method was designed for systems with three-dimensional (3D) periodicity, and not for interfacial systems such as the case of protein adsorption to a charged surface. Interfacial systems such as these have only two-dimensional periodicity, which may not be appropriate for treatment with PME due to the possibility that the presence of multiple charged image surfaces parallel to the primary simulation cell’s surface, may introduce nonphysical effects on the behavior of the charged molecules in the system. In an effort to address this issue, the authors have conducted a set of nanosecond-scale molecular dynamics simulations to calculate the equilibrium distribution of Na+ and Cl− ions near a charged surface using PME and a range of radial cutoff methods for treating electrostatic interactions, where the cutoffs prevent interaction with the periodic images of the system. The resulting ion concentration profiles were compared to one another and to a continuum analytical solution of the theoretical ion distribution obtained from the Poisson—Boltzmann equation. Their results show that the PME method does not introduce the suspected nonphysical effects in the ion distributions due to the 3D periodic images of the system, thus indicating that it is appropriate for use for this type of molecular simulation. Although their interest is motivated by protein-surface interactions, the conclusions are applicable for the treatment of electrostatics in other aqueous systems with two-dimensional periodicity.

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Molecular dynamics studies of solvated polypeptides: Why the cut-off scheme does not work

Cited by 117 publications

References 30 publications

Molecular dynamics simulations of potassium channels

Molecular dynamics simulations of potassium channels

Truncation Effects of Shift Function Methods in Bulk Water Systems

Development of molecular simulation methods to accurately represent protein-surface interactions: Method assessment for the calculation of electrostatic effects

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