. Author manuscript; available in PMC: 2009 Apr 1.

Published in final edited form as: J Chem Theory Comput. 2008 Apr;4(4):549–559. doi: 10.1021/ct700210n

Table 1.

Parameters used in Brownian dynamics simulations. Translational diffusion coefficients (D_tr), number of beads modeling ligands (N_b), hydrodynamic radii (R_HB) of beads, and charge assigned to each bead Q.

molecule	D_tr [ $\frac{c m^{2}}{s}$ ]	N_b	R_HB [Å]	Q
neamine	4.15 · 10⁻⁶	2	4.30	2.0, 2.0
ribostamycin	3.78 · 10⁻⁶	3	4.70	2.0, 2.0, 0.0
paromomycin	3.21 · 10⁻⁶	4	4.40	2.0, 2.0, 0.0, 1.0
neomycin	3.18 · 10⁻⁶	4	4.50	2.0, 2.0, 0.0, 2.0
Mg²⁺	5.71 · 10⁻⁶	1	3.75	2.0
A-site duplex	1.02 · 10⁻⁶