Simulation of the hydration structure of glycyl-alanine

Molecular dynamics (MD) simulations studies have been performed on the aqueous solvation of the dipeptide glycyl-alanine (GA) using classical force-fields AMBER (J. Wang, P. Cieplak, P. A. Kollman, J. Comp. Chem. 21, 1049 (2000)) and CHARMM (N. Foloppe, A. D. MacKerell, J. Comp. Chem. 21, 86 (2000)), and the polarizable force-field AMOEBAPRO (P. Ren, J. W. Ponder, J. Comp. Chem. 23, 1497 (2002), P. Ren, J. W. Ponder, J. Phys. Chem. B. 107, 5933 (2003)). Radial distribution functions and hydration numbers are calculated and compared with the data from Car-Parrinello molecular dynamics (CPMD) and experiments. Our results show all three force-fields can reproduce most of the features of the hydration structure of dipeptide GA. It is also found that AMBER and CHARMM force-fields can describe an averaged chemical environment, while AMOEBAPRO force-field has the capability of capturing the changes in the local environment caused by conformational transitions.