Table 1. Peptide-MHC class II simulation lengths.

	Predisposing		Protective
	C27-FF	A99-FF	C27-FF	A99-FF
MBP (85–98)	120 ns	60 ns	120 ns	60 ns
EBNA-1 (400–413)	120 ns	60 ns	120 ns	60 ns
No-peptide	120 ns	–	120 ns	–

Summary of MHC-peptide complexes modeled with different force fields (C27-FF and A99-FF). MD simulation on free MHC system was done using only C27-FF.