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        Molecular dynamics simulations results of the standard amino acids in aqueous solutions

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        https://doi.org/10.25824/redu/WFFA1W
        https://repositorioslatinoamericanos.uchile.cl/handle/2250/5363156
        Author
        Germiniani, Luiz Guilherme Lomônaco
        Beppu, Marisa Masumi
        Franco, Luís Fernando Mercier
        Institutions
        • Universidade Estadual de Campinas (Brasil)
        Abstract
        Molecular Dynamics simulation results are given in the .xvg files. File names codify the system investigated: - The "VKEETPVd_" stands for the variables: Potential Energy (kJ/mol) Kinetic Energy (kJ/mol) Total Energy (kJ/mol) Conserved Energy (kJ/mol) Temperature (K) Pressure (bar) Volume (nm^3) Density (kg/m^3) - The uppercase letter stands for the amino acid in the mixture and it follows standard abbreviation. - "w" stands for the water, which is the solvent. - Next, there is a set of numbers, which specify the mole fraction composition. In this case, they are the digits after the decimal separator. - Last, the letters "a" or "g" were used to identify the force field used to model the amino acids. "a" stands for the OPLS-AA/M and "g" for the GROMOS 54A7. Example: VKEETPVd_Lw0010a.xvg contains the GROMACS' output data for NPT simulation of aqueous Leucine with 0.0010 mole fraction using OPLS-AA/M force field. We considered only the production data (5 to 10 ns). Standard Amino Acids Abbreviation: G = Glycine A = Alanine V = Valine L = Leucine I = Isoleucine P = Proline F = Phenylalanine Y = Tyrosine W = Tryptophan S = Serine T = Threonine C = Cysteine M = Methionine N = Asparagine Q = Glutamine D = Aspartic Acid (In this work, modeled in the form of Sodium salt) E = Glutamic Acid (In this work, modeled in the form of Sodium salt) K = Lysine (In this work, modeled in the form of Monohydrochloride salt) R = Arginine (In this work, modeled in the form of Monohydrochloride salt) H = Histidine EXCEPTIONS: For pure water simulations were simply named "water".
        Subjects
        Chemistry
        Engineering
        Amino acids
        Molecular dynamics

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        Red de Repositorios Latinoamericanos
        + of 8.000.000
        Available publications
        500 Participating institutions
        Dirección de Servicios de Información y Bibliotecas (SISIB)
        Universidad de Chile
        Membership Login
        Featured collections
        • Latin American Theses
        • Argentinean Theses
        • Chilean Theses
        • Peruvian Theses
        Latest collections added
        • Argentina
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        Dirección de Servicios de Información y Bibliotecas (SISIB)
        Universidad de Chile
        Red de Repositorios Latinoamericanos | 2006-2018