Direct NOE simulation from long MD trajectories

[Display omitted] •A software package is presented which allows calculation of NOEs from long MD trajectories.•The package avoids commonly used assumptions about the distance dependence of NOEs.•Applications to sucrose demonstrate the inseparability of rotational and internal timescales. A software...

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Bibliographic Details
Published in:Journal of magnetic resonance (1997) 2016-04, Vol.265, p.1-9
Main Authors: Chalmers, G., Glushka, J.N., Foley, B.L., Woods, R.J., Prestegard, J.H.
Format: Article
Language:English
Subjects:
Algorithms
Carbohydrate Conformation
Computer Simulation
Fluid dynamics
Inverse
Magnetic Resonance Spectroscopy - methods
Magnetic Resonance Spectroscopy - statistics & numerical data
Mathematical models
Models, Molecular
Molecular dynamics
Molecular Dynamics Simulation
Nuclear Overhauser Effect
Nuclear power generation
Overhauser effect
Simulation
Software
Software packages
Spin relaxation
Sucrose
Sucrose - chemistry
Trajectories
Viscosity
Water - chemistry
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Summary:[Display omitted] •A software package is presented which allows calculation of NOEs from long MD trajectories.•The package avoids commonly used assumptions about the distance dependence of NOEs.•Applications to sucrose demonstrate the inseparability of rotational and internal timescales. A software package, MD2NOE, is presented which calculates Nuclear Overhauser Effect (NOE) build-up curves directly from molecular dynamics (MD) trajectories. It differs from traditional approaches in that it calculates correlation functions directly from the trajectory instead of extracting inverse sixth power distance terms as an intermediate step in calculating NOEs. This is particularly important for molecules that sample conformational states on a timescale similar to molecular reorientation. The package is tested on sucrose and results are shown to differ in small but significant ways from those calculated using an inverse sixth power assumption. Results are also compared to experiment and found to be in reasonable agreement despite an expected underestimation of water viscosity by the water model selected.
ISSN:1090-7807
1096-0856
DOI:10.1016/j.jmr.2016.01.006