Sensitivity of Folding Molecular Dynamics Simulations to Even Minor Force Field Changes.
We examine the sensitivity of folding molecular dynamics simulations on the choice between three variants of the same force field (the AMBER99SB force field and its ILDN, NMR-ILDN, and STAR-ILDN variants). Using two different peptide systems (a marginally stable helical peptide and a β-hairpin) and a grand total of more than 20 μs of simulation time we show that even relatively minor force field changes can lead to appreciable differences in the peptide folding behavior.
Department of Molecular Biology and Genetics, Democritus University of Thrace , University campus, 68100 Alexandroupolis, Greece.
Athanasia-Panagiota
AP
Serafeim
Department of Molecular Biology and Genetics, Democritus University of Thrace , University campus, 68100 Alexandroupolis, Greece.
Georgios
G
Salamanos
Department of Molecular Biology and Genetics, Democritus University of Thrace , University campus, 68100 Alexandroupolis, Greece.
Kalliopi K
KK
Patapati
Department of Molecular Biology and Genetics, Democritus University of Thrace , University campus, 68100 Alexandroupolis, Greece.
Nicholas M
NM
Glykos
D000595:Amino Acid Sequence; D009682:Magnetic Resonance Spectroscopy; D056004:Molecular Dynamics Simulation; D010455:Peptides / Q000737:chemistry*; D017510:Protein Folding; D017433:Protein Structure, Secondary
D010455:Peptides