. Author manuscript; available in PMC: 2019 Nov 21.

Published in final edited form as: J Phys Chem B. 2018 Nov 8;122(46):10455–10469. doi: 10.1021/acs.jpcb.8b09029

Table 1.

Summary of Simulation Setups

Short peptide	Citations BMRB, PDB	Force fields	Simulation number	Length per simulation	Ions	Waters
EGAADAAS	²⁴	ff14SB	10	1 μs	1 Na+	1532-2178
S		ff14IDPSFF	10	1 μs	1 Na+	1465-2569
EGAAEAAS	²⁴	ff14SB	10	1 μs	1 Na+	1628-2622
S		ff14IDPSFF	10	1 μs	1 Na+	1464-3151
EGAAQAAS	²⁴	ff14SB	10	1 μs	1 Na+	1299-2752
S		ff14IDPSFF	10	1 μs	1 Na+	1520-3668
EGAAWAAS	24, 25	ff14SB	10	1 μs	0	1574-2637
S		ff14IDPSFF	10	1 μs	0	1876-3092
EGAAYAAS	²⁴	ff14SB	10	1 μs	0	1804-2867
S		ff14IDPSFF	10	1 μs	0	1888-3141
EGAALAAS	²⁴	ff14SB	10	1 μs	0	1373-3224
S		ff14IDPSFF	10	1 μs	0	1606-3131
EGAAPAAS	²⁴	ff14SB	10	1 μs	0	1751-2713
S		ff14IDPSFF	10	1 μs	0	1693-2885
EGAAHAAS	²⁴	ff14SB	10	1 μs	0	1498-2675
S		ff14IDPSFF	10	1 μs	0	1430-3159
EGAAKAAS	²⁴	ff14SB	10	1 μs	1 Cl−	1733-2434
S		ff14IDPSFF	10	1 μs	1 Cl−	1633-2399
apo Rev (23 amino acids)	(ΔδC^α),³¹	ff14SB	10/50	1 μs / 200 ns	9 Cl−	3727-11638
apo Rev (23 amino acids)	(³J_HNHα),³¹ BRMB:18851³¹	ff14IDPSFF	10/50	1 μs / 200 ns	9 Cl−	4424-13224
RRE - Rev complex	(ΔδC^α),^{30, 38}	ff14SB	5	200 ns	53 Na+ 29 Cl−	10928
RRE - Rev complex	(³J_HNHα),³⁸ PDB:1ETF³⁰	ff14IDPSFF	5	200 ns	53 Na+ 29 Cl−	10928