| 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 |
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| 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 |
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| dc.subject |
Chemistry |
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| dc.subject |
Engineering |
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| dc.title |
Molecular dynamics simulations results of the standard amino acids in aqueous solutions |
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| dc.description.sponsorshipId |
FAPESP: 2018/02713-8 |
|