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. 2020 Mar 12;16(4):2795–2802. doi: 10.1021/acs.jctc.9b01104

Table 1. Structural Parameters of the Peptide.

Tt/Tra (K/K) RMSDb (nm) RMSFc (nm) nHBPPd nHBPWe nHBWWf rgyrg (nm) H2Th (nm) ncl.5%i ncl.95%j
700/700 0.287 ± 0.001 0.29 ± 0.15 0.07 ± 0.03 9.43 ± 0.01 1.17 ± 0.04 0.599 ± 0.001 1.33 ± 0.01 0 2855
600/600 0.279 ± 0.002 0.28 ± 0.15 0.10 ± 0.04 9.90 ± 0.02 1.26 ± 0.05 0.599 ± 0.002 1.28 ± 0.01 0 1850
500/500 0.261 ± 0.002 0.28 ± 0.15 0.20 ± 0.07 10.40 ± 0.03 1.37 ± 0.05 0.561 ± 0.002 1.21 ± 0.01 0 742
400/400 0.243 ± 0.004 0.27 ± 0.14 0.36 ± 0.11 11.31 ± 0.04 1.52 ± 0.05 0.548 ± 0.002 1.16 ± 0.01 2 380
300/300 0.209 ± 0.008 0.24 ± 0.14 0.71 ± 0.14 12.38 ± 0.09 1.72 ± 0.06 0.526 ± 0.002 1.13 ± 0.02 4 80
300/400 0.203 ± 0.009 0.23 ± 0.13 0.84 ± 0.14 12.13 ± 0.10 1.61 ± 0.06 0.520 ± 0.002 1.11 ± 0.02 4 69
300/500 0.215 ± 0.010 0.25 ± 0.13 0.85 ± 0.16 11.85 ± 0.12 1.48 ± 0.08 0.520 ± 0.003 1.10 ± 0.02 5 72
300/600 0.186 ± 0.010 0.22 ± 0.12 1.25 ± 0.20 10.70 ± 0.11 1.35 ± 0.07 0.501 ± 0.002 1.04 ± 0.01 5 26
300/700 0.184 ± 0.012 0.22 ± 0.12 1.54 ± 0.22 10.09 ± 0.10 1.24 ± 0.07 0.493 ± 0.002 1.00 ± 0.02 5 26
a

Translational (Tt) and rotational (Tr) temperatures of the solvent during MD simulation.

b

Average trajectory root mean square deviation (RMSD) value compared to the experimentally determined peptide reference structure.24,25

c

Average trajectory root mean square fluctuations (RMSF) of the peptide backbone.

d

Average number of native structure-forming intrapeptide hydrogen bonds.

e

Average number of intermolecular hydrogen bonds between the peptide and water molecules.

f

Average number of intermolecular hydrogen bonds between the water molecules per molecule.

g

Average peptide radius of gyration.

h

Average head-to-tail distance of the peptide.

i

Number of peptide structural clusters that are stable for at least 5% of the simulation time.

j

Number of structural clusters that encompass 95% of the trajectory.