ct3006248_si_001.pdf (594.94 kB)
Comparison of Three Chain-of-States Methods: Nudged Elastic Band and Replica Path with Restraints or Constraints
journal contribution
posted on 2012-12-11, 00:00 authored by Peng Tao, Milan Hodošček, Joseph D. Larkin, Yihan Shao, Bernard R. BrooksChain-of-state methods are becoming important tools in
studying
the chemical reaction mechanisms, especially for biomacromolecules.
In this article, three chain-of-state methods, the nudged elastic
band (NEB) method and the replica path method with restraints or constraints,
were tested and compared using three model systems with various sizes
and at different levels of theory: alanine dipeptide isomerization,
β-alanine intramolecular condensation, and the matrix metalloproteinase
2 inhibition mechanism. The levels of theory used to describe the
three model systems include molecular mechanics (MM), quantum mechanics
(QM), and combined quantum mechanics and molecular mechanics (QM/MM).
All three methods could correctly determine a reaction path with reasonable
estimation of reaction barriers in most cases. The RMSD measurement
with additional weighting schemes provides practically infinite choices
of reaction coordinates to describe the reaction progress. These findings
demonstrate that the chain-of-state methods are powerful tools when
being used carefully to generate a plausible reaction mechanism with
full pathway for complex systems at an affordable computational cost.