Ecosyste.ms: Awesome
An open API service indexing awesome lists of open source software.
https://github.com/simongravelle/peggenerator
Generate PEG topology for GROMACS and LAMMPS
https://github.com/simongravelle/peggenerator
gromacs lammps molecular-dynamics peg polyethylene-glycol python3
Last synced: 3 months ago
JSON representation
Generate PEG topology for GROMACS and LAMMPS
- Host: GitHub
- URL: https://github.com/simongravelle/peggenerator
- Owner: simongravelle
- License: gpl-3.0
- Created: 2021-12-23T13:14:27.000Z (about 3 years ago)
- Default Branch: main
- Last Pushed: 2024-08-19T10:44:37.000Z (5 months ago)
- Last Synced: 2024-08-19T12:39:22.966Z (5 months ago)
- Topics: gromacs, lammps, molecular-dynamics, peg, polyethylene-glycol, python3
- Language: Jupyter Notebook
- Homepage:
- Size: 511 KB
- Stars: 17
- Watchers: 2
- Forks: 6
- Open Issues: 1
-
Metadata Files:
- Readme: README.md
- License: LICENSE
Awesome Lists containing this project
README
[](https://zenodo.org/doi/10.5281/zenodo.13341575)
[](https://www.gnu.org/licenses/gpl-3.0)
# Generate PEG topology for GROMACS and LAMMPS
### Description
Python scripts for generating a single all-atom PEG (-OH terminated) or PEG (-CH3 terminated) molecule with a number Nseg
of monomer. The charmm36 force field is used, and the output is readable by GROMACS
and LAMMPS.
### How to (for GROMACS):
Generate the configuration files using generatePEGgromacs.ipynb, or simply by executing generatepeg.sh
from the GROMACS folder:
```
sh generatepeg_gromacs.sh
```
You can vary the number of monomer by changing the value of Nseg. Then, minimize the energy of the PEG using GROMACS:
```
gmx grompp -f input/em.mdp -o em -pp em -po em
gmx mdrun -v -deffnm em
mv em.gro conf.gro
```
Eventually, you can relaxe the PEG molecule in the NVT ensemble:
```
gmx grompp -f input/nvt.mdp -o nvt -pp nvt -po nvt
gmx mdrun -v -deffnm nvt
```
### Output (GROMACS)
Pre-equilibrated topology files are given here :
* [PEG200](GROMACS/PEG200/)
* [PEG600](GROMACS/PEG600/)
* [PEG1200](GROMACS/PEG1200/)
This [video](https://www.youtube.com/watch?v=FkFdO58UdOA) has been made using
the PEG molecule generated with this script.
### Contact
Feel free to contact me by email if you have inquiries. You can find contact
details on my [personal page](https://simongravelle.github.io/).