Dependence of A-RNA simulations on the choice of the force field and salt strength
| Authors | |
|---|---|
| Year of publication | 2009 |
| Type | Article in Periodical |
| Magazine / Source | Physical Chemistry Chemical Physics |
| MU Faculty or unit | |
| Citation | |
| Field | Biophysics |
| Keywords | molecular dynamics methods; RNA; force field; A-form |
| Description | We carried out an extensive molecular dynamics study on three A-RNA duplexes. Dependence of the A-RNA geometry on force fields (Parm99 and Parmbsc0) and salt strength conditions was investigated. The Parmbsc0 force field makes the A-RNA duplex more compact in comparison to the Parm99 by preventing temporary alfa/gama t/t flips common in Parm99 simulations. The stabilization of the A-RNA helices caused by the Parmbsc0 force field includes visible reduction of the major groove width, increase of the base pair roll, larger helical inclination and small increases of twist. Therefore, the Parmbsc0 shifts the simulated duplexes more deeply into the A-form. |
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