Using molecular dynamics trajectories to predict nuclear spin relaxation behaviour in large spin systems
Using molecular dynamics trajectories to predict nuclear spin relaxation behaviour in large spin systems
Molecular dynamics (MD) trajectories provide useful insights into molecular structure and dynamics. However, questions persist about the quantitative accuracy of those insights. Experimental NMR spin relaxation rates can be used as tests, but only if relaxation superoperators can be efficiently computed from MD trajectories – no mean feat for the quantum Liouville space formalism where matrix dimensions quadruple with each added spin 1/2. Here we report a module for the Spinach software framework that computes Bloch-Redfield-Wangsness relaxation superoperators (including non-secular terms and cross-correlations) from MD trajectories. Predicted initial slopes of nuclear Overhauser effects for sucrose trajectories using advanced water models and a force field optimised for glycans are within 25% of experimental values.
Spin relaxation, Molecular dynamics, Water models, Glycan force fields
Kuprov, Ilya
bb07f28a-5038-4524-8146-e3fc8344c065
Morris, Laura C
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Glushka, John N.
e21a2f78-4ebe-4213-9dc8-ed3a1843d88f
Prestegard, James H.
00c5b6c8-8774-4497-b1ae-9c001af7f869
Kuprov, Ilya
bb07f28a-5038-4524-8146-e3fc8344c065
Morris, Laura C
b338dd2d-e8b2-4440-9f13-3439c5e32a56
Glushka, John N.
e21a2f78-4ebe-4213-9dc8-ed3a1843d88f
Prestegard, James H.
00c5b6c8-8774-4497-b1ae-9c001af7f869
Kuprov, Ilya, Morris, Laura C, Glushka, John N. and Prestegard, James H.
(2020)
Using molecular dynamics trajectories to predict nuclear spin relaxation behaviour in large spin systems.
Journal of Magnetic Resonance, 323.
(doi:10.1016/j.jmr.2020.106891).
Abstract
Molecular dynamics (MD) trajectories provide useful insights into molecular structure and dynamics. However, questions persist about the quantitative accuracy of those insights. Experimental NMR spin relaxation rates can be used as tests, but only if relaxation superoperators can be efficiently computed from MD trajectories – no mean feat for the quantum Liouville space formalism where matrix dimensions quadruple with each added spin 1/2. Here we report a module for the Spinach software framework that computes Bloch-Redfield-Wangsness relaxation superoperators (including non-secular terms and cross-correlations) from MD trajectories. Predicted initial slopes of nuclear Overhauser effects for sucrose trajectories using advanced water models and a force field optimised for glycans are within 25% of experimental values.
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Accepted/In Press date: 8 December 2020
e-pub ahead of print date: 13 December 2020
Keywords:
Spin relaxation, Molecular dynamics, Water models, Glycan force fields
Identifiers
Local EPrints ID: 446488
URI: http://eprints.soton.ac.uk/id/eprint/446488
ISSN: 1090-7807
PURE UUID: d3bce957-ebd8-44e3-bca5-9d7eac9eb518
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Date deposited: 11 Feb 2021 17:33
Last modified: 17 Mar 2024 06:17
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Contributors
Author:
Laura C Morris
Author:
John N. Glushka
Author:
James H. Prestegard
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