Simulation Foundry for Methanol-Water Mixtures

Determination of thermophysical properties (densities, diffusion coefficients, energy contributions) of different methanol-water mixtures using molecular dynamics simulations.

DOI: 10.15490/fairdomhub.1.study.639.1

Zenodo URL: None

Created at: 7th Nov 2019 at 12:28

Contents

Preparation

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.

Installation Instructions

Follow the instructions in this file to get the necessary software packages to run the Simulation Foundry Version 1.5.

INSTALLATIONINSTRUCTIONS.txt

KNOWN ISSUES

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.

KNOWNISSUES.txt

Manual V1.5

Manual to Simulation Foundry Version 1.5.

MANUAL_V1.5.docx

oplsaa.ff

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 )

oplsaa.ff.zip

DirectoryStructure

Screenshot of the directory structure required for the Simulation Foundry.

Directory.PNG

Simulation Version 1.5

This is the simulation part of the Simulation Foundry, Version 1.5.

Download and unpack the zip file and the .sh bash script. Copy them into a folder which has a meaningful name.
Launch the bash script, following the instructions in the manual.

Make sure you followed the instructions in "Preparation" before running this.

SIMULATIONS_V1.5

Master Bash script to launch Molecular Dynamics when running the Simulation part of Simulation Foundry.
Make sure you followed "Preparations" instructions!
Read the Manual!

SIMULATIONS_V1.5.sh

SIMULATION_V1.5

Scripts and Input Files for Simulation V1.5

SIMULATION_V1.5.zip

Analysis Version 1.5

This is the analysis part of the Simulation Foundry, Version 1.5.

Download and unpack the zip file and the .sh bash script. Copy them into a folder which has a meaningful name.
Launch the bash script, following the instructions in the manual.

Make sure you followed the instructions in "Preparation" before running this.

ANALYSIS_1.5

Master Bash script to launch Molecular Dynamics when running the Analysis part of Simulation Foundry.
Make sure you followed "Preparations" instructions!
Read the Manual!