Wei Zhang

TL;DR: A third‐generation point‐charge all‐atom force field for proteins is developed and initial tests on peptides demonstrated a high‐degree of similarity between the calculated and the statistically measured Ramanchandran maps for both Ace‐Gly‐nme and Ace‐Ala‐Nme di‐peptides.

TL;DR: Examining the accuracy and efficiency of REMD by examining its ability to reproduce the results of multiple extended conventional molecular dynamics simulations and to enhance conformational sampling shows that REMD can accurately reproduce long-time MD results with high efficiency.

TL;DR: The formation mechanism of an alanine-based peptide has been studied by all- atom molecular dynamics simulations with a recently developed all-atom point-charge force field and the Generalize Born continuum solvent model and an extrapolated folding time of 16-20 ns is obtained in qualitative agreement with experiments.

TL;DR: Detailed folding processes and mechanisms of two alanine-based peptides were investigated by all atom molecular dynamic simulation with a new AMBER force field and Generalized Born continuum solvent model and it was found that helix−turn−helix conformation was the most stable state at 300 K, instead of the expected full helix conformed.

TL;DR: An automatic algorithm for assigning chemical connectivity and bond order regardless of hydrogen for organic molecules is provided, and only three dimensional coordinates and element identities are needed for the algorithm.