MindSPONGE

Description

MindSPONGE (MindSpore Simulation Package tOwards Next Generation molecular modelling)

Software Architecture

Installation

This code was developed base on the AI framework MindSpore: https://mindspore.cn/en

• Install the dependency libraries:

pip install -r requirements.txt

• Compile the codes:

export CUDA_PATH={your_cuda_path}
bash build.sh -e gpu -j32

• The compiled whl package is in the dist directory. Use pip to install:

pip install mindsponge-[gpu|ascend]

Instructions

The tutorials for user are in the "tutorials" directory：

Basic tutorials:

tutorial_b01.py: Create a simple simulation system manually.

tutorial_b02.py: Create a simple simulation system using template and parameters file.

tutorial_b03.py: Edit system and minimization.

tutorial_b04.py: MD simulation with bias potential.

tutorial_b05.py: MD simulation with periodic boundary condition.

tutorial_b06.py: Minimization and MD simulation of protein molecule.

tutorial_b07.py: Constraint and LINCS.

Advanced tutorials:

tutorial_a01.py: Metrics and collective variables (CVs).

tutorial_a02.py: Bias potential and metadynamics (MetaD)

tutorial_a03.py: Energy wrapper and integrated tempering sampling (ITS).

tutorial_a04.py: Hybrid enhanced sampling and MetaITS

Contribution

1. Fork the repository
2. Create Feat_xxx branch
3. Commit your code
4. Create Pull Request

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