Molecular dynamics simulations in crystalline environments have emerged as an important class of methods that have led to a number of important scientific advances ranging from aiding in the interpretation of experimental structural data to testing the reliability of predicted solution structural relaxations. Recently it has become clear that crystal simulations provide robust tests for the reliability of force fields by means of better sampling both inter- and intramolecular structure and dynamics, as well as a direct comparison to experimental data. Therefore, it is essential to construct a proper protocol for carrying out crystal simulations, and subsequently assess the capabilities of current force fields in reproducing the experimental observables. To do so for nucleic acids, we have selected a set of DNA double helix systems that samples all the major helical families of DNA (i.e. A-DNA, B-DNA, and Z-DNA) and various chain lengths of B-DNA, the most common family. We report the results of these crystal simulations and assess the reliability and the limitations of current nucleic acid force fields in reproducing structure and fluctuations in crystalline environments.

Simulating nucleic acids in their crystal environment: A test for gauging accuracy of modern force fields

255th National Meeting (2018)

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