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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.
History
Journal
Molecular simulationVolume
33Issue
4-5Pagination
337 - 342Publisher
Taylor & FrancisLocation
Abingdon, Eng.Publisher DOI
ISSN
0892-7022eISSN
1029-0435Language
engPublication classification
C1.1 Refereed article in a scholarly journalCopyright notice
2007, Taylor & FrancisUsage metrics
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