Molecular dynamics simulations of proteins in solution: Artifacts caused by the cutoff approximation

Saito, Minoru

doi:10.1063/1.468411

Cited by 111 publications

(75 citation statements)

References 17 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The long-range nonbonded interactions also were treated differently: a 16 Å nonbond cutoff was imposed in MD1, whereas in MD2 long-range Coulombic interactions were calculated without a cutoff by using the PPPC method. 43,44 Uncertainties in the MD1 S 2 values were calculated from the 900-ps trajectory by using a ''jacknife'' algorithm 45,25 and a sampling window of 90 ps.…”

Section: Methodsmentioning

confidence: 99%

Accuracy and precision of NMR relaxation experiments and MD simulations for characterizing protein dynamics

et al. 1997

View full text Add to dashboard Cite

Model-free parameters obtained from nuclear magnetic resonance (NMR) relaxation experiments and molecular dynamics (MD) simulations commonly are used to describe the intramolecular dynamical properties of proteins. To assess the relative accuracy and precision of experimental and simulated model-free parameters, three independent data sets derived from backbone 15N NMR relaxation experiments and two independent data sets derived from MD simulations of Escherichia-coli ribonuclease HI are compared. The widths of the distributions of the differences between the order parameters for pairs of NMR data sets are congruent with the uncertainties derived from statistical analyses of individual data sets; thus, current protocols for analyzing NMR data encapsulate random uncertainties appropriately. Large differences in order parameters for certain residues are attributed to systematic differences between samples for intralaboratory comparisons and unknown, possibly magnetic field-dependent, experimental effects for interlaboratory comparisons. The widths of distributions of the differences between the order parameters for two NMR sets are similar to widths of distributions for an NMR and an MD set or for two MD sets. The linear correlations between the order parameters for an MD set and an NMR set are within the range of correlations observed between pairs of NMR sets. These comparisons suggest that the NMR and MD generalized order parameters for the backbone amide N-H bond vectors are of comparable accuracy for residues exhibiting motions on a fast time scale (< 100 ps). Large discrepancies between NMR and MD order parameters for certain residues are attributed to the occurrence of "rare" motional events over the simulation trajectories, the disruption of an element of secondary structure in one of the simulations, and lack of consensus among the experimental data sets. Consequently, (easily detectable) severe distortions of local protein structure and infrequent motional events in MD simulations appear to be the most serious artifacts affecting the accuracy and precision, respectively, of MD order parameters relative to NMR values. In addition, MD order parameters for motions on a fast (< 100 ps) timescale are more precisely determined than their NMR counterparts, thereby permitting more detailed dynamic characterization of biologically important residues by MD simulation than is sometimes possible by experimental methods. Proteins 28:481-493, 1997.

show abstract

Section: Methodsmentioning

confidence: 99%

Accuracy and precision of NMR relaxation experiments and MD simulations for characterizing protein dynamics

et al. 1997

View full text Add to dashboard Cite

show abstract

“…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

View full text Add to dashboard Cite

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.

show abstract

“…However, the critical issue to the short-range treatment is to improve its accuracy and remove the possible artifacts arising in it. [10][11][12][13][14] As one of the approaches to address this issue in a shortrange treatment, [15][16][17][18][19][20][21][22][23][24][25][26][27][28][29] the zero-multipole (summation) method (ZMM) has been developed. 30 The underlying physical idea is simple, as follows.…”

Section: Introductionmentioning

confidence: 99%

A critical appraisal of the zero-multipole method: Structural, thermodynamic, dielectric, and dynamical properties of a water system

Wang

Nakamura

Fukuda

2016

The Journal of Chemical Physics

View full text Add to dashboard Cite

THE JOURNAL OF CHEMICAL PHYSICS 144, 114503 (2016) A critical appraisal of the zero-multipole method: Structural, thermodynamic, dielectric, and dynamical properties of a water system We performed extensive and strict tests for the reliability of the zero-multipole (summation) method (ZMM), which is a method for estimating the electrostatic interactions among charged particles in a classical physical system, by investigating a set of various physical quantities. This set covers a broad range of water properties, including the thermodynamic properties (pressure, excess chemical potential, constant volume/pressure heat capacity, isothermal compressibility, and thermal expansion coefficient), dielectric properties (dielectric constant and Kirkwood-G factor), dynamical properties (diffusion constant and viscosity), and the structural property (radial distribution function). We selected a bulk water system, the most important solvent, and applied the widely used TIP3P model to this test. In result, the ZMM works well for almost all cases, compared with the smooth particle mesh Ewald (SPME) method that was carefully optimized. In particular, at cut-off radius of 1.2 nm, the recommended choices of ZMM parameters for the TIP3P system are α ≤ 1 nm −1 for the splitting parameter and l = 2 or l = 3 for the order of the multipole moment. We discussed the origin of the deviations of the ZMM and found that they are intimately related to the deviations of the equilibrated densities between the ZMM and SPME, while the magnitude of the density deviations is very small. C 2016 Author(s). All article content, except where otherwise noted, is licensed under a Creative Commons Attribution (CC BY) license

show abstract

Molecular dynamics simulations of proteins in solution: Artifacts caused by the cutoff approximation

Cited by 111 publications

References 17 publications

Accuracy and precision of NMR relaxation experiments and MD simulations for characterizing protein dynamics

Accuracy and precision of NMR relaxation experiments and MD simulations for characterizing protein dynamics

Truncation Effects of Shift Function Methods in Bulk Water Systems

A critical appraisal of the zero-multipole method: Structural, thermodynamic, dielectric, and dynamical properties of a water system

Contact Info

Product

Resources

About