TABLE 2.

Distances between K⁺ and the nearest backbone carbonyl oxygen atoms are reported for NMR (R_NMR), MD_GA (R_{MD_GA}) and MD_GA_K (R_{MD_GA_K}) configurations

Name and no. of the residue	RNMR (Å)	RMD_GA (Å)	RMD_GA_K (Å)	ΔRNMR (Å)	ΔRMD (Å)	ΔαMD (deg)
FOR0	3.95	4.30	4.25	0.30	−0.05	6
VAL1	4.03	4.01	3.30	−0.73	−0.71	24
ALA3	3.07	3.35	2.87	−0.20	−0.48	14
FOR17	3.95	3.99	4.03	0.08	0.04	17
VAL18	4.04	4.11	3.13	−0.91	−0.98	33
ALA20	3.09	3.35	2.89	−0.2	−0.46	15

For the NMR configuration, K⁺ was placed in the center of the channel. For the MD_GA configuration, Gramicidin A was equilibrated with only water in the channel, then the average configuration over the trajectory was generated, and a K⁺ ion placed in the center of the channel. To generate the MD_GA_K configuration, Gramicidin A was equilibrated by MD simulation with K⁺ placed at the center of the channel, fixing the coordinate in the axial direction; then the average configuration over the trajectory was generated. Changes in K⁺-carbonyl oxygen distances between NMR and MD_GA_K (ΔR_NMR) configurations and between MD_GA and MD_GA_K (ΔR_MD) configurations are also given in the Table, as are changes in the carbonyl group angles (Δα_MD) between MD_GA and MD_GA_K configurations. The name and the number of the corresponding residues are given in the first column of the table and are enumerated as in the original file (1GRM) taken from the protein data bank (www.rcsb.org).