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AI2BMD is an artificial intelligence-based ab initio biomolecular dynamics system.
[Nature](https://www.nature.com/articles/s41586-024-08127-z) | [Github](https://github.com/microsoft/AI2BMD)

# 1. Description
AI2BMD has the same accuracy with QM and faster running speed (one order slower than MM).

# 2. Installation
According to Prof. Wang's response ([Github issue 20](https://github.com/microsoft/AI2BMD/issues/20)), the software can only be installed with Docker.

## 2.1 Install Docker with apt
[Docker Docs](https://docs.docker.com/engine/install/)

- (1) add apt source
```
# Add Docker's official GPG key:
sudo apt-get update
sudo apt-get install ca-certificates curl
sudo install -m 0755 -d /etc/apt/keyrings
sudo curl -fsSL https://download.docker.com/linux/ubuntu/gpg -o /etc/apt/keyrings/docker.asc
sudo chmod a+r /etc/apt/keyrings/docker.asc
```
```
# Add the repository to Apt sources:
echo \
  "deb [arch=$(dpkg --print-architecture) signed-by=/etc/apt/keyrings/docker.asc] https://download.docker.com/linux/ubuntu \
  $(. /etc/os-release && echo "$VERSION_CODENAME") stable" | \
  sudo tee /etc/apt/sources.list.d/docker.list > /dev/null
sudo apt-get update
```

- (2) install Docker-ce
```
sudo apt-get install docker-ce docker-ce-cli containerd.io docker-buildx-plugin docker-compose-plugin
```

- (3) Update openssl (Optional)

  [REF](https://developer.baidu.com/article/detail.html?id=2891342). I encounter the error (curl: (35) OpenSSL SSL_connect: Connection reset by peer in connection to download.docker.com:443). 
```
sudo apt-get upgrade openssl
```

- (4) Add mirror link

  [ref](https://github.com/DaoCloud/public-image-mirror) To download docker image domestically. 
```
# add lines below into /etc/docker/daemon.json
{
  "registry-mirrors": [
    "https://docker.m.daocloud.io"
  ]
}
```
```
# apply the daemon configurations
sudo systemctl daemon-reload
sudo systemctl restart docker
```

- (5) verify the installation
```
sudo docker run hello-world
```

- (6) install nvidia container toolkit

  [Ref](https://docs.nvidia.com/datacenter/cloud-native/container-toolkit/latest/install-guide.html#installing-with-apt) This toolkit is needed if cuda is used in Docker image. Add the apt source, update index and install the package. 
```
curl -fsSL https://nvidia.github.io/libnvidia-container/gpgkey | sudo gpg --dearmor -o /usr/share/keyrings/nvidia-container-toolkit-keyring.gpg \
  && curl -s -L https://nvidia.github.io/libnvidia-container/stable/deb/nvidia-container-toolkit.list | \
    sed 's#deb https://#deb [signed-by=/usr/share/keyrings/nvidia-container-toolkit-keyring.gpg] https://#g' | \
    sudo tee /etc/apt/sources.list.d/nvidia-container-toolkit.list
```
```
sudo apt-get update
sudo apt-get install -y nvidia-container-toolkit
```
  [REF](https://blog.csdn.net/qq_38628046/article/details/136312844) To fix the error "could not select device driver ““ with capabilities: [[gpu]]". 
```
sudo nvidia-ctk runtime configure --runtime=docker
sudo vi /etc/docker/daemon.json
sudo systemctl restart docker
```

- (7) Add permission for one user (Optional)
  
  Everytime you change the configuration (add one user, modify the daemon.json and so on), restart the server and print the status.
```
sudo groupadd docker
sudo usermod -aG docker $USER
newgrp docker
sudo systemctl restart docker
sudo systemctl status docker
```

## 2.2 Pull AI2BMD docker image
[REF](https://github.com/microsoft/AI2BMD)

- (1) Pull the image
```
# add sudo to the command if the user doesn't have the permission
# or just add the permission following the instruction above
# it may take ~2 hours (a faster mirror link or the VPN may help a lot in this step)
docker pull ghcr.io/microsoft/ai2bmd:latest
```

- (2) Get the software
```
wget 'https://raw.githubusercontent.com/microsoft/AI2BMD/main/scripts/ai2bmd'
chmod +x ai2bmd
```
It is recommended to put the script in your PATH, such as `/home/usr/bin`

- (3) Get the test system
```
# download the Chignolin protein structure data file
wget 'https://raw.githubusercontent.com/microsoft/AI2BMD/main/examples/chig.pdb'
# download the preprocessed and solvated Chignolin protein structure data files
wget --directory-prefix=chig_preprocessed 'https://raw.githubusercontent.com/microsoft/AI2BMD/main/examples/chig_preprocessed/chig-preeq.pdb'
wget --directory-prefix=chig_preprocessed 'https://raw.githubusercontent.com/microsoft/AI2BMD/main/examples/chig_preprocessed/chig-preeq-nowat.pdb'
```

- (4) Run it !
```
ai2bmd --prot-file chig.pdb --preprocess-dir chig_preprocessed --preeq-steps 0 --sim-steps 1000 --record-per-steps 1 --gpus 0
# I add the option --gpus, otherwise all cards will be called. The envirionment variable 'CUDA_VISIBLE_DEVICE' won't work.
# Use './ai2bmd' to call the script if it's not put into the PATH
# Use 'sudo ./ai2bmd' if the permission is not added to the user
```


# 3. Usage


# 4. Notes

There is one problem not solved. The files generated have the permission `root:root`, so one normal user can't delete the folder...

I have serched online to find the solution but failed to get an elegant one.

I raised a [Github issue](https://github.com/microsoft/AI2BMD/issues/51), waiting for Prof. Wang's reply.
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