diff --git a/README.md b/README.md
index d474a91b5..ddf13902b 100644
--- a/README.md
+++ b/README.md
@@ -34,10 +34,9 @@ DOI: 10.1021/acs.jctc.2c01297`
 
 ## Developer Guide
 + [1. Introduction](docs/dev_guide/introduction.md)
-+ [2. Software architecture](docs/dev_guide/arch.md)
-+ [3. Coding conventions](docs/dev_guide/convention.md)
-+ [4. Document writing](docs/dev_guide/write_docs.md)
-+ [5. An example for developing: how to write a generator?](docs/dev_guide/generator.ipynb)
++ [2. Coding conventions](docs/dev_guide/convention.md)
++ [3. Document writing](docs/dev_guide/write_docs.md)
++ [4. An example for developing: how to write a generator?](docs/dev_guide/generator.ipynb)
 
 ## Code Structure
 
diff --git a/docs/user_guide/2.installation.md b/docs/user_guide/2.installation.md
index bf361d5d5..d2e21cebf 100644
--- a/docs/user_guide/2.installation.md
+++ b/docs/user_guide/2.installation.md
@@ -17,6 +17,12 @@ pip install "jax[cuda11_local]==0.4.14" -f https://storage.googleapis.com/jax-re
 conda install -c conda-forge mdtraj==1.9.7
 pip install optax==0.1.3 pymbar==4.0.1 jaxopt==0.8.1
 ```
++ Install [mdtraj](https://github.com/mdtraj/mdtraj), [optax](https://github.com/deepmind/optax) and [pymbar](https://github.com/choderalab/pymbar):
+```bash
+conda install -c conda-forge mdtraj==1.9.7
+pip install optax==0.1.3
+pip install pymbar==4.0.1
+```
 + Install [OpenMM](https://openmm.org/):
 ```bash
 conda install -c conda-forge openmm==7.7.0