https://github.com/becksteinlab/alchemical_conformational_analysis
https://github.com/becksteinlab/alchemical_conformational_analysis
Last synced: 3 months ago
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- Host: GitHub
- URL: https://github.com/becksteinlab/alchemical_conformational_analysis
- Owner: Becksteinlab
- Created: 2021-06-25T02:02:03.000Z (almost 4 years ago)
- Default Branch: main
- Last Pushed: 2021-09-11T00:56:00.000Z (over 3 years ago)
- Last Synced: 2025-01-06T10:48:27.787Z (5 months ago)
- Language: Jupyter Notebook
- Size: 5.57 MB
- Stars: 0
- Watchers: 3
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
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README
# Conformational Analysis of SAMPL7 molecules
Start with SM46 (see submitted paper).
Bogdan created timeseries for the two main dihedrals (see tar file on spudda,
too big for repo).
To set up:
bash ./bin/RSYNC
bash ./bin/SETUP
You can then use the notebooks in analysis.
You need a conda environment with
- alchemlyb
- pandas
- matplotlib
- numpy
- tqdm
- seaborn
## Raw data
Generated with `gmx angle` (see `GROMACS_ANALYZE_dihedral_analysis`):
```bash
gmx angle -type dihedral -f $i/md.xtc -n $ff-dih1.ndx -od $j-dih1-dist.xvg -ov $j-dih1-ts.xvg
gmx angle -type dihedral -f $i/md.xtc -n $ff-dih2.ndx -od $j-dih2-dist.xvg -ov $j-dih2-ts.xvg
```
### CGENFF and OPLS-AA (mol2ff)
Tar file with data.
* `spudda.beckstein.physics.asu.edu:/nfs/homes/bogdan/Projects/SAMPL7-PhysProp/_dih_analysis.tgz`
Use `bin/RSYNC.sh` to get the data.
### GAFF and LigParGen
Shujie generated the data
* `yamsolo.beckstein.physics.asu.edu:/nfs/homes3/sfan/Projects/SAMPL7/_dih_gaff`
* `yamsolo.beckstein.physics.asu.edu:/nfs/homes3/sfan/Projects/SAMPL7/_dih_ligpargen`