Dynamic properties of force fields

F. Vitalini, A. S.J.S. Mey, F. Noé, B. G. Keller

Research output: Contribution to journalArticlepeer-review

Abstract / Description of output

Molecular-dynamics simulations are increasingly used to study dynamic properties of biological systems. With this development, the ability of force fields to successfully predict relaxation timescales and the associated conformational exchange processes moves into focus. We assess to what extent the dynamic properties of model peptides (Ac-A-NHMe, Ac-V-NHMe, AVAVA, A10) differ when simulated with different force fields (AMBER ff99SB-ILDN, AMBER ff03, OPLS-AA/L, CHARMM27, and GROMOS43a1). The dynamic properties are extracted using Markov state models. For single-residue models (Ac-A-NHMe, Ac-V-NHMe), the slow conformational exchange processes are similar in all force fields, but the associated relaxation timescales differ by up to an order of magnitude. For the peptide systems, not only the relaxation timescales, but also the conformational exchange processes differ considerably across force fields. This finding calls the significance of dynamic interpretations of molecular-dynamics simulations into question.

Original languageEnglish
Article number084101
JournalJournal of Chemical Physics
Volume142
Issue number8
Early online date24 Feb 2015
DOIs
Publication statusE-pub ahead of print - 24 Feb 2015

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