Preparation needed to use Simulation Foundry, Version 1.5.
Please read the manual before working with this Simulation Foundry.
Pay careful attention to the installation instructions.
Note the known issues.
Expertise: enzyme kinetics, enzymes, Enzymatic reactions, biochemical enzyme characterization, Biochemistry, molecular simulation, molecular modeling, Programming, Bioinformatics, Computational Biology
Tools: Gromacs, Python, Molecular Dynamics, bash, Biochemistry, Bioinformatics, Biochemistry and protein analysis, Enzyme assay, enzyme kinetics, isothermal titration calorimetry, dynamic light scattering, Spectrophotometry
Well rounded biologist/biotechnologist/biochemist/enzymologist/bioinformatician/computational biologist.
Determination of thermophysical properties (densities, diffusion coefficients, energy contributions) of different methanol-water mixtures using molecular dynamics simulations.
Person responsible: Gudrun Gygli
Follow the instructions in this file to get the necessary software packages to run the Simulation Foundry Version 1.5.
This is a list of errors that can be produced if the Simulation Foundry is not used correctly - the messages are cryptic, hopefully the file is helpful to some.
OPLSAA force field used by GROMACS on the BINAC Supercomputer (chem/gromacs/5.1.4-gnu-4.9, https://wiki.bwhpc.de/e/Category:BwForCluster_BinAC )