Conformational dynamics of trialanine in water. 2. Comparison of AMBER, CHARMM, GROMOS, and OPLS force fields to NMR and infrared experiments

Mu, Yuguang, Kosov, Daniil S., and Stock, Gerhard (2003) Conformational dynamics of trialanine in water. 2. Comparison of AMBER, CHARMM, GROMOS, and OPLS force fields to NMR and infrared experiments. Journal of Physical Chemistry Part B, 107 (21). pp. 5064-5073.

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Abstract

Driven by recent two-dimensional infrared experiments by Woutersen and Hamm, trialanine has emerged as a paradigm to study conformational dynamics of a small peptide in aqueous solution. Employing the exceptional amount of experimental and ab initio data, in this work, trialanine serves as a model problem to perform a comprehensive comparison of six popular force fields, including the recent versions of the AMBER, CHARMM, GROMOS, and OPLS models. For all force fields under consideration, 20 ns long molecular-dynamics simulations are performed, and the structure and conformational dynamics of the solvated peptide is studied in detail. Employing density-functional theory calculations at the B3LYP/6-31+G(d) level, a number of observable quantities are calculated directly from the molecular-dynamics data and compared to experiment. The comparison allows for a quite detailed interpretation of recent NMR and infrared experiments. The nowadays achievable reliability and accuracy of a molecular dynamics description of a highly flexible biomolecular system are discussed in some detail.

Item ID: 26481
Item Type: Article (Research - C1)
ISSN: 1520-5207
Date Deposited: 23 Jun 2013 23:09
FoR Codes: 02 PHYSICAL SCIENCES > 0204 Condensed Matter Physics > 020405 Soft Condensed Matter @ 50%
03 CHEMICAL SCIENCES > 0307 Theoretical and Computational Chemistry > 030704 Statistical Mechanics in Chemistry @ 50%
SEO Codes: 97 EXPANDING KNOWLEDGE > 970102 Expanding Knowledge in the Physical Sciences @ 100%
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