https://github.com/simongravelle/graphene-oxide-at-water-interface
https://github.com/simongravelle/graphene-oxide-at-water-interface
Last synced: 7 months ago
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- Host: GitHub
- URL: https://github.com/simongravelle/graphene-oxide-at-water-interface
- Owner: simongravelle
- License: gpl-3.0
- Created: 2021-09-05T07:56:19.000Z (about 4 years ago)
- Default Branch: main
- Last Pushed: 2021-11-01T20:15:11.000Z (about 4 years ago)
- Last Synced: 2025-03-29T13:11:18.582Z (8 months ago)
- Language: C
- Size: 13.8 MB
- Stars: 5
- Watchers: 2
- Forks: 3
- Open Issues: 1
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Metadata Files:
- Readme: README.md
- License: LICENSE
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README
# Adsorption of graphene oxide nanoparticles at the water vapor interface
This scipts can be used to measure the free energy profile of a GO nanoparticle at the interface between water and vapor.
## Step 1. LAMMPS input file generation
Go in the consruction folder and run GenerateData.m using Matlab. It may also work with Octave. You can select a different graphene oxide nanoparticle from this [bank of nanoparticle](https://github.com/simongravelle/GrapheneOxideNanoparticle). It will create 29 folders and 29 input files, all corresponding to a different initial position for the GO nanoparticle.
## Step 2. Run lammps
Run the input.lammps in all 29 folders using LAMMPS software. If you are new to LAMMPS, you can find [tutorials here](https://lammpstutorials.github.io/) that include help for free energy calculation.
## Step 3. Run the wham algorithm
To extract the positions of the particles from the generated data, run the wham algorithm from the Wham folder:
./wham -28 28 45 1e-8 300 0 metadata.dat PMF.dat 5 455878
The PMF file contains the free energy profile along the z axis across the interface. The wham algorithm is from [GROSSFIELD lab](http://membrane.urmc.rochester.edu/?page_id=126)
If you use this work, please cite:
[Gravelle S.](https://simongravelle.github.io/) and [Botto L.](https://bottogroup.wordpress.com/), [Adsorption of single and multiple graphene oxide nanoparticles at a water-vapor interface, Langmuir](https://pubs.acs.org/doi/10.1021/acs.langmuir.1c01902)