Abstract
The free-energy profile for the conformational isomerization process in alanine dipeptide is presented in atomistic detail by using an action-derived molecular dynamics (ADMD) method and replica-exchange molecular dynamics (REMD) method. First, by employing ADMD, a dynamic isomerization pathway model of the alanine dipeptide with two available low-energy conformations, C7 ax and C7 eq , is determined. The pathway model is chosen to be the reaction coordinate, so the isomerization process is characterized by the ADMD step index, which is not an a-priori reaction coordinate as found in conventional studies of molecular conformational changes. Second, by employing the REMD method, the free-energy profile is calculated as a function of temperature. This couple of procedures is a quite natural protocol for conformational isomerization process simulations, irrespective of the arbitrary selection of the reaction coordinate. The alliance between the two simulation methods, ADMD and REMD, is demonstrated to have a great synergy effect on understanding the conformational changes in molecules.
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