| Name | dpamber JSON |
| Version |
0.4.0
JSON |
| download |
| home_page | |
| Summary | Some useful tools related to Amber and DP. |
| upload_time | 2023-09-09 01:00:12 |
| maintainer | |
| docs_url | None |
| author | |
| requires_python | >=3.7 |
| license | |
| keywords |
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| VCS |
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|
| requirements |
No requirements were recorded.
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# dpamber
Some useful tools related to Amber and DP.
## Installation
```sh
pip install dpamber
```
## Tools
### corr: generating data for DPRc models
[](https://doi.org/10.1021/acs.jctc.1c00201)
[](https://doi.org/10.1021/acs.jctc.1c00201)
`corr` tool generates [DeePMD-kit](https://github.com/deepmodeling/deepmd-kit) training data for DPRc from AMBER sander low-level QM/MM data and high-level data. For details of DPRc, read the [DPRc paper](https://doi.org/10.1021/acs.jctc.1c00201).
Before using this tool, one need to prepare low-level and high-level QM/MM data:
$$
E_\text{hl}(\mathbf R)=E_\text{hl,QM}(\mathbf R)+E_\text{hl,QM/MM}(\mathbf R)+E_\text{MM}(\mathbf R)
$$
$$
E_\text{ll}(\mathbf R)=E_\text{ll,QM}(\mathbf R)+E_\text{ll,QM/MM}(\mathbf R)+E_\text{MM}(\mathbf R)
$$
Low-level and high-level data should use the same coordinate and the same MM method, but different QM methods. So, the correction energy for training will be
$$
\Delta E (\mathbf R) = E_\text{hl}(\mathbf R) - E_\text{ll}(\mathbf R) = (E_\text{hl,QM}(\mathbf R) - E_\text{ll,QM}(\mathbf R)) + (E_\text{hl,QM/MM}(\mathbf R) - E_\text{ll,QM/MM}(\mathbf R))
$$
An example of the command is
```sh
dpamber corr --cutoff 6. --qm_region ":1" --parm7_file some_param.param7 --nc some_coord.nc --hl high_level --ll low_level --out dataset
```
where `--cutoff` takes cutoff radius of the QM/MM interaction for training. `--qm_region` takes AMBER mask format for the QM region. `--parm7_file` and `--nc` take the PARM7 file and the trajectory (NetCDF) file, respectively. `--ll` and `--hl` are the prefixes of low-level and high-level files, including the mdout file (`.mdout`), the mden file (`.mden`) and the mdfrc file (`.mdfrc`). The output dataset directory should be put in `--out`.
See details from `dpamber corr -h`.
### devi: calculate model deviation
`devi` can be used to calculate the model deviation of a given trajectory.
You need to install DeePMD-kit using
```sh
pip install dpamber[dpgpu]
```
See `dpamber devi -h` for details.
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"description": "# dpamber\n\nSome useful tools related to Amber and DP.\n\n## Installation\n\n```sh\npip install dpamber\n```\n\n## Tools\n### corr: generating data for DPRc models\n\n[](https://doi.org/10.1021/acs.jctc.1c00201)\n[](https://doi.org/10.1021/acs.jctc.1c00201)\n\n`corr` tool generates [DeePMD-kit](https://github.com/deepmodeling/deepmd-kit) training data for DPRc from AMBER sander low-level QM/MM data and high-level data. For details of DPRc, read the [DPRc paper](https://doi.org/10.1021/acs.jctc.1c00201).\n\nBefore using this tool, one need to prepare low-level and high-level QM/MM data:\n\n$$\nE_\\text{hl}(\\mathbf R)=E_\\text{hl,QM}(\\mathbf R)+E_\\text{hl,QM/MM}(\\mathbf R)+E_\\text{MM}(\\mathbf R)\n$$\n\n$$\nE_\\text{ll}(\\mathbf R)=E_\\text{ll,QM}(\\mathbf R)+E_\\text{ll,QM/MM}(\\mathbf R)+E_\\text{MM}(\\mathbf R)\n$$\n\nLow-level and high-level data should use the same coordinate and the same MM method, but different QM methods. So, the correction energy for training will be\n\n$$\n\\Delta E (\\mathbf R) = E_\\text{hl}(\\mathbf R) - E_\\text{ll}(\\mathbf R) = (E_\\text{hl,QM}(\\mathbf R) - E_\\text{ll,QM}(\\mathbf R)) + (E_\\text{hl,QM/MM}(\\mathbf R) - E_\\text{ll,QM/MM}(\\mathbf R))\n$$\n\nAn example of the command is\n```sh\ndpamber corr --cutoff 6. --qm_region \":1\" --parm7_file some_param.param7 --nc some_coord.nc --hl high_level --ll low_level --out dataset\n```\nwhere `--cutoff` takes cutoff radius of the QM/MM interaction for training. `--qm_region` takes AMBER mask format for the QM region. `--parm7_file` and `--nc` take the PARM7 file and the trajectory (NetCDF) file, respectively. `--ll` and `--hl` are the prefixes of low-level and high-level files, including the mdout file (`.mdout`), the mden file (`.mden`) and the mdfrc file (`.mdfrc`). The output dataset directory should be put in `--out`.\n\nSee details from `dpamber corr -h`.\n\n### devi: calculate model deviation\n\n`devi` can be used to calculate the model deviation of a given trajectory.\nYou need to install DeePMD-kit using\n```sh\npip install dpamber[dpgpu]\n```\n\nSee `dpamber devi -h` for details.\n",
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