Direct NOE Simulation from Long MD Trajectories

Overview

Journal J Magn Reson

Publisher Elsevier

Date 2016 Feb 1

PMID 26826977

Citations 14

Authors

G Chalmers

J N Glushka

B L Foley

R J Woods

J H Prestegard

Affiliations

Soon will be listed here.

Abstract

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.

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