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

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dc.contributor.author Germiniani, Luiz Guilherme Lomônaco
dc.contributor.author Beppu, Marisa Masumi
dc.contributor.author Franco, Luís Fernando Mercier
dc.date 2021-08-17
dc.date.accessioned 2021-08-16
dc.identifier.uri https://doi.org/10.25824/redu/WFFA1W
dc.identifier.uri https://redu.unicamp.br/dataset.xhtml?persistentId=doi:10.25824/redu/WFFA1W
dc.description 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".
dc.description.sponsorship Fundação de Amparo à Pesquisa do Estado de São Paulo
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dc.publisher Mercier Franco, Luís Fernando
dc.subject Chemistry
dc.subject Engineering
dc.title Molecular dynamics simulations results of the standard amino acids in aqueous solutions
dc.description.sponsorshipId FAPESP: 2018/02713-8


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