Conformational dynamics of an alanine dipeptide analog: An ab initio molecular dynamics study - art. no. 011907

An ab initio molecular dynamics (MD) simulation technique employing the Bor n-Oppenheimer approach in the framework of a Gaussian implementation of Koh n-Sham density functional theory is used to study the gas-phase conformatio nal dynamics of an alanine dipeptide analog. It is found that conformationa l transformation between C5 and C7(eq) occurs on the picosecond time scale. Classical MD simulations using most of the popular force fields do not yie ld a transition even after nanoseconds. An analysis is given of the differe nce, for this small gas-phase system. between ab initio MD and traditional MD simulation using force fields.