Accelerated molecular
dynamics (aMD) protocols were assessed on
predicting the secondary structure of eight peptides, of which two
are helical, three are β-hairpins, and three are disordered.
Protocols consisted of combinations of three force fields (ff99SB,
ff14SB, ff19SB) and two explicit solvation models (TIP3P and OPC),
and were evaluated in two independent aMD simulations, one starting
from an extended conformation, the other starting from a misfolded
conformation. The results of these analyses indicate that all three
combinations performed well on helical peptides. As for β-hairpins,
ff19SB performed well with both solvation methods, with a slight preference
for the TIP3P solvation model, even though performance was dependent
on both peptide sequence and initial conformation. The ff19SB/OPC
combination had the best performance on intrinsically disordered peptides.
In general, ff14SB/TIP3P suffered the strongest helical bias.