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https://github.com/deepmodeling/DeePDih
Deep Potential driven molecular dihedral scan toolkit
https://github.com/deepmodeling/DeePDih
Last synced: 2 months ago
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Deep Potential driven molecular dihedral scan toolkit
- Host: GitHub
- URL: https://github.com/deepmodeling/DeePDih
- Owner: deepmodeling
- License: mit
- Created: 2024-03-03T13:22:19.000Z (10 months ago)
- Default Branch: main
- Last Pushed: 2024-06-23T14:34:36.000Z (7 months ago)
- Last Synced: 2024-07-31T09:11:06.952Z (5 months ago)
- Language: Python
- Size: 5.57 MB
- Stars: 3
- Watchers: 2
- Forks: 2
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
Awesome Lists containing this project
- deepmodeling-projects - GitHub
README
# DeePDih
Deep Potential driven dihedral scan toolkit.
## Installation
### Requirements
- Python 3.8 or later (3.10 recommended)
- PyTorch 2
- DeePMD-kit (at least 3.0.0a0)
- networkx
- RDKit
- ASE
- Geometric
- DPData
- OpenMM (for adding bias and reading Gromacs topology)
- tblite (for semi-empirical level geometry optimization)
- Psi4 (for high-level quantum mechanical single point energy)
### Install requirements using conda
Users can install the required packages by running the following command:
```bash
conda install -c conda-forge rdkit geometric tblite-python psi4 openmm
```
If you want to use Psi4 to compute RESP charges, you also need to install Psi4 with the following command:
```bash
conda install -c psi4 psi4
```
### Install requirements from PyPI
```bash
pip install ase dpdata networkx
```
If you want to use Gromacs topology, you also need to install ambertools, acpype and parmed.
```bash
conda install -c conda-forge ambertools
pip install acpype parmed
```
### Install requirements from source
#### DeePMd-kit
Please look at DeePMD-kit's [installation guide](https://github.com/deepmodeling/deepmd-kit/releases/tag/v3.0.0a0)
#### Geometric-jit
Accelerate Geometric using Numba and JIT. Please look at [this repository](https://github.com/WangXinyan940/geomeTRIC_jit).
Numba is also needed if you want to use the JIT version of Geometric.
```bash
conda install -c conda-forge numba
```
### Install DeePDih module from source
```bash
pip install .
```