Table 3. Comparison between 10 ns Simulations in Explicit Solvent (expl), Implicit Solvent Using the New Parametrization Derived Here (impl.n), and Implicit Solvent Using the Old Parametrization (impl.o)^a.

protein	SASAtotal (nm2)	SASAphob (nm2)	SASAphil (nm2)	Rgyr (nm)	rmsd (nm)	rmsf (nm)
trpexpl	14.37	8.56	5.81	0.75*	0.34*	0.17*
trpimpl.n	16.97	10.09	6.88	0.73	0.23	0.12
trpimpl.o	18.24	10.52	7.73	0.77	0.31	0.12
drkexpl	42.55	21.95	20.61	1.11*	0.31*	0.13*
drkimpl.n	42.25	22.67	19.58	1.06	0.27	0.11
drkimpl.o	45.88	23.14	22.74	1.07	0.23	0.08
ubqexpl	53.27	29.96	23.31	1.21*	0.26*	0.12*
ubqimpl.n	51.00	27.63	23.37	1.15	0.38	0.17
ubqimpl.o	55.90	29.26	26.64	1.19	0.28	0.12
if3cexpl	61.64	35.67	25.97	1.34*	0.18*	0.11*
if3cimpl.n	64.47	34.34	30.14	1.28	0.27	0.11
if3cimpl.o	67.87	35.53	32.34	1.30	0.29	0.15
lysexpl	68.00	37.18	30.82	1.41*	0.23*	0.15*
lysimpl.n	68.96	35.50	33.46	1.35	0.29	0.12
lysimpl.o	77.93	38.73	39.20	1.40	0.33	0.12
talinexpl	115.24	67.45	47.80	1.92*	0.48*	0.19*
talinimpl.n	107.53	61.08	46.44	1.90	0.39	0.14
talinimpl.o	115.04	63.77	51.27	1.91	0.38	0.12

^aThe test proteins (PDB code) are trp (1l2y), drk (2a36), ubq (1ubq), if3c (1tig), lys (1aki), and talin (2jsw). Values marked with an asterisk and trajectories underlying the expl SASA values were taken from Allison et al.²⁴ R_gyr: radius of gyration; rmsd: root mean square deviation from the X-ray or NMR model structure; rmsf: root mean square fluctuation.