From 66496e338f230d1739de38c8ed76efb5ff0b0908 Mon Sep 17 00:00:00 2001 From: Jinzhe Zeng Date: Tue, 19 Dec 2023 16:53:26 -0500 Subject: [PATCH 1/2] docs: update Amber interface Merge after AmberTools24 is published. Signed-off-by: Jinzhe Zeng --- doc/third-party/out-of-deepmd-kit.md | 12 +++++++++--- 1 file changed, 9 insertions(+), 3 deletions(-) diff --git a/doc/third-party/out-of-deepmd-kit.md b/doc/third-party/out-of-deepmd-kit.md index 3d46b53578..0d26dcb490 100644 --- a/doc/third-party/out-of-deepmd-kit.md +++ b/doc/third-party/out-of-deepmd-kit.md @@ -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://gitlab.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 From 10371c64920dff47f2c4db14e7e16fa4e92e8f2a Mon Sep 17 00:00:00 2001 From: Jinzhe Zeng Date: Tue, 19 Dec 2023 16:55:35 -0500 Subject: [PATCH 2/2] fix the url of dpamber Signed-off-by: Jinzhe Zeng --- doc/third-party/out-of-deepmd-kit.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/doc/third-party/out-of-deepmd-kit.md b/doc/third-party/out-of-deepmd-kit.md index 0d26dcb490..ca5c7437fb 100644 --- a/doc/third-party/out-of-deepmd-kit.md +++ b/doc/third-party/out-of-deepmd-kit.md @@ -26,7 +26,7 @@ The DPRc model and the interface were developed by the [York Lab](https://theory 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://gitlab.com/njzjz/dpamber/), a tiny tool to convert Amber trajectory to DPRc training data; +- [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