← Search

Data · dataset · 2022

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

Listed in REDU - Unicamp Institutional Research Data Repository

Molecular Dynamics simulation results are given in the .xvg files.

Description

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).

Read the rest (1 more)

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".

Links

Where it is published

Catalogue records · 1

Topics

Stated by source
Chemistry · Engineering
Provenance · 1 source records, 13 field assertions
SourceKeyLast seenRaw
REDU - Unicamp Institutional Research Data Repositorydoi:10.25824/redu/WFFA1W12 d agoJSON v1
FieldAssertionExtractorEvidence
concepts[field].anzsrc:group:3404enrichment · redu unicamp brtaxonomy-embedding@1.1.0title+keywords+description (71%)
concepts[field].dataverse_subject:chemistrysource · redu unicamp brconnector:redu_unicamp_br@1.0.0/subjects
concepts[field].dataverse_subject:engineeringsource · redu unicamp brconnector:redu_unicamp_br@1.0.0/subjects
concepts[field].local:field:chemistrymapping · redu unicamp brconnector:redu_unicamp_br@1.0.0/subjects
concepts[field].local:field:engineeringmapping · redu unicamp brconnector:redu_unicamp_br@1.0.0/subjects
concepts[field].local:field:life-sciencesmapping · redu unicamp brconnector:redu_unicamp_br@1.0.0/subjects
concepts[method].local:method:simulationenrichment · redu unicamp brkeyword-concept-rules@1.0.0title+description (75%)
created_datesource · redu unicamp brconnector:redu_unicamp_br@1.0.0
descriptionsource · redu unicamp brconnector:redu_unicamp_br@1.0.0/description
publication_datesource · redu unicamp brconnector:redu_unicamp_br@1.0.0
titlesource · redu unicamp brconnector:redu_unicamp_br@1.0.0/name
updated_datesource · redu unicamp brconnector:redu_unicamp_br@1.0.0
version_labelsource · redu unicamp brconnector:redu_unicamp_br@1.0.0