TABLE 4.

Average number of hydrogen bonds formed at the early and late stages of the simulations for protein-lipid pairs, protein-water pairs, lipid-water pairs, and intramolecular peptide hydrogen bonds

	Protein-lipid		Protein-water		Lipid-water		Protein-protein
Run	0–1 ns	5–10 ns	0–1 ns	5–10 ns	0–1 ns	5–10 ns	0–1 ns	5–10 ns
PER1	3.2	9.9	38.4	31.7	394	369	12	8.7
PER2	9.1	14.4	34.1	23.2	406	387	10.9	7.1
PER3	5.3	17.1	27.4	16.0	405	385	14.6	13.5
PAR1	14.8	19.4	19.9	11.8	400	388	11.8	11.9
PAR2	10.1	15.3	30.3	20.1	407	387	9.3	8.4
PAR3	16.2	28.1	27.8	15.5	397	368	6.0	5.8
PAR4	9.3	22.3	31.7	19.0	397	367	8.8	7.0
PAR5	14.5	17.8	12.7	11.1	388	372	13.8	13.1
MUT1	4.9	9.7	36.3	28.5	403	395	8.9	7.9
MUT2	1.6	5.4	26.3	21.5	400	378	13.3	8.0
MUT3	3.1	6.1	21.1	11.6	407	380	11.3	10.2
MUT4	3.6	11.8	31.3	23.6	403	382	12.3	7.9
MUT5	8.1	17.9	30.6	18.5	405	382	10.7	8.9

For the beginning of the simulations, the first nanosecond is averaged and for the late stages of the simulation, the last 5 ns are averaged. For simulation PER1, the last 10 ns are averaged for the late stages. The general trend is for the number of protein-lipid hydrogen bonds to increase with time, the protein-water and lipid-water hydrogen bonds to decrease with time, and the intramolecular protein hydrogen bonds to stay constant or slightly decrease with time. The standard deviations in all the values in this table are approximately of the magnitude 1. Hence, comparisons of early and late stages of a given simulation are indeed statistically valid (except, in some cases, protein-protein interactions).