| dc.contributor | Mercier Franco, Luís Fernando | |
| dc.creator | Germiniani, Luiz Guilherme Lomônaco | |
| dc.creator | Beppu, Marisa Masumi | |
| dc.creator | Franco, Luís Fernando Mercier | |
| dc.date.accessioned | 2022-12-16T13:22:51Z | |
| dc.date.available | 2022-12-16T13:22:51Z | |
| dc.identifier | https://doi.org/10.25824/redu/WFFA1W | |
| dc.identifier.uri | https://repositorioslatinoamericanos.uchile.cl/handle/2250/5363156 | |
| 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.publisher | Repositório de Dados de Pesquisa da Unicamp | |
| dc.subject | Chemistry | |
| dc.subject | Engineering | |
| dc.subject | Amino acids | |
| dc.subject | Molecular dynamics | |
| dc.title | Molecular dynamics simulations results of the standard amino acids in aqueous solutions | |
