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
- Dataverse dataset page redu.unicamp.br/dataset.xhtml?persistentId=doi%3A10.25824%2Fredu%2FWFFA1W ↗
landing page · from redu unicamp br
- DOI doi.org/10.25824/redu/wffa1w ↗
DOI / persistent id · from redu unicamp br
Catalogue records · 1
- Dataverse API redu.unicamp.br/api/datasets/:persistentId/?persistentId=doi%3A10.25824%2Fredu… ↗
metadata API · from redu unicamp br
Topics
- Stated by source
- Chemistry · Engineering
- From keywords
- Chemistry · Engineering · Life Sciences
- Inferred from text
- Medicinal and biomolecular chemistry 71% · Simulation 75%
Provenance · 1 source records, 13 field assertions
| Source | Key | Last seen | Raw |
|---|---|---|---|
| REDU - Unicamp Institutional Research Data Repository | doi:10.25824/redu/WFFA1W | 13 d ago | JSON v1 |
| Field | Assertion | Extractor | Evidence |
|---|---|---|---|
| concepts[field].anzsrc:group:3404 | enrichment · redu unicamp br | taxonomy-embedding@1.1.0 | title+keywords+description (71%) |
| concepts[field].dataverse_subject:chemistry | source · redu unicamp br | connector:redu_unicamp_br@1.0.0 | /subjects |
| concepts[field].dataverse_subject:engineering | source · redu unicamp br | connector:redu_unicamp_br@1.0.0 | /subjects |
| concepts[field].local:field:chemistry | mapping · redu unicamp br | connector:redu_unicamp_br@1.0.0 | /subjects |
| concepts[field].local:field:engineering | mapping · redu unicamp br | connector:redu_unicamp_br@1.0.0 | /subjects |
| concepts[field].local:field:life-sciences | mapping · redu unicamp br | connector:redu_unicamp_br@1.0.0 | /subjects |
| concepts[method].local:method:simulation | enrichment · redu unicamp br | keyword-concept-rules@1.0.0 | title+description (75%) |
| created_date | source · redu unicamp br | connector:redu_unicamp_br@1.0.0 | |
| description | source · redu unicamp br | connector:redu_unicamp_br@1.0.0 | /description |
| publication_date | source · redu unicamp br | connector:redu_unicamp_br@1.0.0 | |
| title | source · redu unicamp br | connector:redu_unicamp_br@1.0.0 | /name |
| updated_date | source · redu unicamp br | connector:redu_unicamp_br@1.0.0 | |
| version_label | source · redu unicamp br | connector:redu_unicamp_br@1.0.0 |