. 2016 Jun 14;12(8):4114–4127. doi: 10.1021/acs.jctc.6b00186

Table 2. Root-Mean-Square Deviations (RMSDs) (in Å) of Average Structures from Molecular Dynamics Simulations with Respect to the NMR Reference Structure of the Drew–Dickerson Dodecamer (DDD)^a.

	bsc0	bsc1	OL15	CHARMM36	CHARMM36-JC^b
TIP3P	1.00	0.64	0.53	1.29	1.30
OPC	0.91	0.61	0.44

The average structure from simulations for each system was calculated over the full aggregated trajectory for that system; the DDD NMR reference was an average of the models in the 1NAJ structure. RMSDs were calculated over all heavy atoms of the internal eight base pairs.

CHARMM36-JC refers to the simulations with the Joung-Cheatham ion parameters.

Table 2. Root-Mean-Square Deviations (RMSDs) (in Å) of Average Structures from Molecular Dynamics Simulations with Respect to the NMR Reference Structure of the Drew–Dickerson Dodecamer (DDD)a.

Table 2. Root-Mean-Square Deviations (RMSDs) (in Å) of Average Structures from Molecular Dynamics Simulations with Respect to the NMR Reference Structure of the Drew–Dickerson Dodecamer (DDD)^a.