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.
SEEK ID: https://fairdomhub.org/assays/1146
Projects: Simulation Foundries
Investigation: hidden item
Assay type: Instructions
Technology type: Technical Computer Installation
Organisms: No organisms
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
Polyglot European Scientist. I thrive working in interdisciplinary environments combining the study of enzyme reactions and mechanisms with bioinformatics, molecular modelling, automated data analysis and data stewardship.
Determination of thermophysical properties (densities, diffusion coefficients, energy contributions) of different methanol-water mixtures using molecular dynamics simulations.
Submitter: Gudrun Gygli
Investigation: 1 hidden item
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 )