Conformational Dynamics of Trialanine in Water. 2. Comparison of AMBER, CHARMM, GROMOS, and OPLS Force Fields to NMR and Infrared Experiments
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 p...
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| Published in: | The journal of physical chemistry. B Vol. 107; no. 21; pp. 5064 - 5073 |
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| Format: | Journal Article |
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American Chemical Society
29-05-2003
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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. |
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| AbstractList | 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. |
| Author | Stock, Gerhard Mu Kosov, Daniil S |
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| Title | Conformational Dynamics of Trialanine in Water. 2. Comparison of AMBER, CHARMM, GROMOS, and OPLS Force Fields to NMR and Infrared Experiments |
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