Molecular dynamics simulations results of the standard amino acids in aqueous solutions
Autor
Germiniani, Luiz Guilherme Lomônaco
Beppu, Marisa Masumi
Franco, Luís Fernando Mercier
Institución
Resumen
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".