Table V.
Comparative analysis of conformational statistics for alanine dipeptide
| SCCDFTB amber 1 |
SCCDFTB Charmm221 |
amber1 | charmm21 | cedar1 | gromos1 | oplsaa1 | oplsaa/l2 | absinth3 | |
|---|---|---|---|---|---|---|---|---|---|
| beta | 0.48 | 0.48 | 0.16 | 0.50 | 0.71 | 0.82 | 0.86 | 0.69 | 0.50 |
| pass | 0.16 | 0.14 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.06 | 0.09 |
| alpha R | 0.27 | 0.33 | 0.84 | 0.50 | 0.22 | 0.13 | 0.14 | 0.25 | 0.39 |
| alpha L | 0.07 | 0.03 | 0.00 | 0.00 | 0.05 | 0.04 | 0.00 | 0.00 | 0.01 |
| state 4 | 0.01 | 0.01 | 0.00 | 0.00 | 0.02 | 0.01 | 0.00 | 0.00 | 0.01 |
| RMSDI4 | 0.00 | 0.08 | 0.68 | 0.29 | 0.29 | 0.40 | 0.44 | 0.24 | 0.15 |
| MaxDI5 | 0.00 | 0.06 | 0.57 | 0.23 | 0.23 | 0.34 | 0.38 | 0.21 | 0.12 |
| RMSDII6 | 0.08 | 0.00 | 0.62 | 0.22 | 0.29 | 0.42 | 0.45 | 0.24 | 0.08 |
| MaxDII7 | 0.06 | 0.00 | 0.51 | 0.17 | 0.23 | 0.34 | 0.38 | 0.21 | 0.06 |
Data for conformational statistics shown in columns 2-8 are taken from Tables I and II in the work of Hu et al..78
Values for conformational statistics were computed using molecular dynamics simulations. In these simulations, we used parameters from the OPLS-AA/L force field for the peptide and the TIP3P model for water molecules. The simulations were carried out with a single alanine dipeptide in a cubic box of side 25Å. The Berendsen thermostat (T=298K; coupling constant 0.1ps) and manostat (P=1bar; coupling constant, 1ps) were used to simulate the peptide in water in an isothermal-isobaric ensemble. The SETTLE algorithm was used to constrain bond lengths and bond angles for the water molecules, whereas the LINCS method was used to constrain all bond lengths in the peptide. A time step of 2.0fs was used and the equations of motion were integrated using the leap frog method as implemented in the GROMACS package. A 10Å spherical cutoff was used for both van der Waals and electrostatic interactions. Neighbor lists were updated once every five time steps and a reaction field with a bulk dielectric constant of 80 was used as a method to introduce corrections due to long-range electrostatic interactions. Data shown in the table are averages over 40 independent simulations, each of length 30ns.
Values for conformational statistics were obtained using Metropolis Monte Carlo simulations. Details of the move sets used are shown in Table III.
RMSDI is the root-mean-square deviation between statistics shown in columns 2-10 (for the five conformational states) and the statistics shown in column 2 (SCCDFTB – amber).
MAXDI is the unsigned maximal deviation between statistics shown in columns 2-10 and the statistics shown in column 2 (SCCDFTB-amber).
RMSDII is the root-mean-square deviation between statistics shown in columns 2-10 (for the five conformational states) and the statistics shown in column 3 (SCCDFTB – charmm22).
MAXDII is the unsigned maximal deviation between statistics shown in columns 2-10 and the statistics shown in column 3 (SCCDFTB-charmm22).