Conformational dynamics of an alanine dipeptide analog: an ab initio molecular dynamics study.
An ab initio molecular dynamics (MD) simulation technique employing the Born-Oppenheimer approach in the framework of a Gaussian implementation of Kohn-Sham density functional theory is used to study the gas-phase conformational dynamics of an alanine dipeptide analog. It is found that conformational transformation between C5 and C7(eq) occurs on the picosecond time scale. Classical MD simulations using most of the popular force fields do not yield a transition even after nanoseconds. An analysis is given of the difference, for this small gas-phase system, between ab initio MD and traditional MD simulation using force fields.
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D000409:Alanine / Q000737:chemistry*; D002467:Cell Nucleus / Q000378:metabolism; D003198:Computer Simulation; D006860:Hydrogen Bonding; D007700:Kinetics; D008954:Models, Biological; D008958:Models, Molecular; D016011:Normal Distribution; D010455:Peptides / Q000737:chemistry*; D011487:Protein Conformation; D012984:Software; D013696:Temperature; D013997:Time Factors
D010455:Peptides; D000409:Alanine