| Abstract: | The relative free energies of hydration of the dipeptides glycylalanine and alanyl‐glycine in their naturally occurring form have been calculated both for the zwitterionic and protonated species. Emphasis was laid on comparisons between the conventional cutoff method and the Particle Mesh Ewald method to account for possible differences in electrostatic contributions to the free energy. Furthermore, the convergence behavior of the total free energy and its individual contributions were examined. The results, obtained by means of the thermodynamic integration technique as implemented in the free energy module of the AMBER program suite, suggest that in aqueous solution glycylalanine is more stable than alanylglycine by 2.7 kcal/mol in the zwitterionic form and by 3.5 kcal/mol in the protonated form. © 2001 John Wiley & Sons, Inc. J Comput Chem 22: 846–860, 2001 |
