Skip to content

docs: update Amber interface #3074

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
njzjz merged 2 commits into from
Jan 20, 2024
Merged

docs: update Amber interface #3074

Changes from all commits
Commits
Show all changes
2 commits
Select commit Hold shift + click to select a range
66496e3
docs: update Amber interface
njzjz Dec 19, 2023
10371c6
fix the url of dpamber
njzjz Dec 19, 2023
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
12 changes: 9 additions & 3 deletions doc/third-party/out-of-deepmd-kit.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -19,9 +19,15 @@ By inferring with the DP model `frozen_model_compressed.pb`, dpdata will generat

An [OpenMM](https://github.com/openmm/openmm) plugin is provided from [JingHuangLab/openmm_deepmd_plugin](https://github.com/JingHuangLab/openmm_deepmd_plugin), written by the [Huang Lab](http://www.compbiophysics.org/) at Westlake University.

## AMBER interface to DeePMD-kit

An [AMBER](https://ambermd.org/) interface to DeePMD-kit is written by the [York [Lab](https://theory.rutgers.edu/) from Rutgers University. It is open-source at [GitLab RutgersLBSR/AmberDPRc](https://gitlab.com/RutgersLBSR/AmberDPRc/). Details can be found in [this paper](https://doi.org/10.1021/acs.jctc.1c00201).
## Amber interface to DeePMD-kit

Starting from [AmberTools24](https://ambermd.org/), `sander` includes an interface to the DeePMD-kit, which implements the [Deep Potential Range Corrected (DPRc) correction](../model/dprc.md).
The DPRc model and the interface were developed by the [York Lab](https://theory.rutgers.edu/) from Rutgers University.
More details are available in
- [Amber Reference Manuals](https://ambermd.org/Manuals.php), providing documentation for how to enable the interface and the `&dprc` namelist;
- [GitLab RutgersLBSR/AmberDPRc](https://gitlab.com/RutgersLBSR/AmberDPRc/), providing examples mdin files;
- [DP-Amber](https://github.com/njzjz/dpamber/), a tiny tool to convert Amber trajectory to DPRc training data;
- [The original DPRc paper](https://doi.org/10.1021/acs.jctc.1c00201).

## DP-GEN

Expand Down