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
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
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
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!
- ANALYSIS_V1.5.sh
Results
These are the results from the Analysis part of the Simulation foundry.
QualityControl
Overview of the quality control checks obtained from the Simulation Foundry.
- QualityControl.pdf
These checksums allow you to check a Snapshot you have downloaded hasn't been modified. For details on how to use these please visit this guide
MD5: 1cb387642ee21355ef23971e978657f3
SHA1: a970e0a9d916c9f424ab81db60268add3520fa4a
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Created: 7th Nov 2019 at 12:28
Last updated: 14th Apr 2020 at 06:47