CONSTRUCTING A MODEL FOR PERFORMING SIMULATION OF THE MOLECULAR DYNAMICS OF A PEPTIDE IN VACUUM

ADRIANA ISVORAN

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CONSTRUCTING A MODEL FOR PERFORMING SIMULATION OF THE MOLECULAR DYNAMICS OF A PEPTIDE IN VACUUM

机译：建立真空中肽的分子动力学模拟模型

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The aim of this work is to construct a molecular model of the polyalanine peptide for energy and force calculations in absence of the solvent to characterise the built model and to analyse the effects of the mutations on the geometry and the sta-bility of the peptid.

机译：这项工作的目的是在没有溶剂的情况下构建用于能量和力计算的聚丙氨酸肽的分子模型，以表征所构建的模型并分析突变对肽的几何形状和稳定性的影响。

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《Romanian journal of physics》 |2002年第6期|p.657-661|共5页
作者
ADRIANA ISVORAN;
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West University of Timisoara, Department of Physics, Blvd. V. Parvan no. 4, 1900 Timisoara;

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正文语种 eng
中图分类物理学;
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4. Dynamic effects on peptide structure: molecular dynamics simulations of a peptide employing ensemble of peptides [C] . Kaur, K. . 2005

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5. Molecular dynamics simulations of collagen model peptides: Implication for collagen diseases and recognition. [D] . Fu, Iwen. 2015

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7. The thermodynamic changes that occur upon mixing five models of formamide and three models of water, including the miscibility of these model combinations itself, is studied by performing Monte Carlo computer simulations using an appropriately chosen thermodynamic cycle and the method of thermodynamic integration. The results show that the mixing of these two components is close to the ideal mixing, as both the energy and entropy of mixing turn out to be rather close to the ideal term in the entire composition range. Concerning the energy of mixing, the OPLS/AA-mod model of formamide behaves in a qualitatively different way than the other models considered. Thus, this model results in negative, while the other ones in positive energy of mixing values in combination with all three water models considered. Experimental data supports this latter behavior. Although the Helmholtz free energy of mixing always turns out to be negative in the entire composition range, the majority of the model combinations tested either show limited miscibility, or, at least, approach the miscibility limit very closely in certain compositions. Concerning both the miscibility and the energy of mixing of these model combinations, we recommend the use of the combination of the CHARMM formamide and TIP4P water models in simulations of water-formamide mixtures. [O] . Kiss, Bálint, Fábián, Balázs, Idrissi, Abdenacer, 2017

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CONSTRUCTING A MODEL FOR PERFORMING SIMULATION OF THE MOLECULAR DYNAMICS OF A PEPTIDE IN VACUUM

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