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 13:28

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!

  • ANALYSIS_V1.5.sh

ANALYSIS_V1.5

Scripts and Input Files for Analysis V1.5

  • ANALYSIS_V1.5.zip

Results

These are the results from the Analysis part of the Simulation foundry.

Results

Overview of the results obtained from the Simulation Foundry.

  • Results.pdf

QualityControl

Overview of the quality control checks obtained from the Simulation Foundry.

  • QualityControl.pdf
Fingerprints

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

Citation
Gygli, G., & Pleiss, J. (2020). Simulation Foundry for Methanol-Water Mixtures. FAIRDOMHub. https://doi.org/10.15490/FAIRDOMHUB.1.STUDY.639.1
Snapshots
Snapshot 2 (24th Mar 2020) DOI
Snapshot 1 (7th Nov 2019) DOI
Activity

Views: 770   Downloads: 18

Created: 7th Nov 2019 at 13:28

Last updated: 14th Apr 2020 at 08:47

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