From 2023197bbdc07df43c146c2d201052dc505b8a9c Mon Sep 17 00:00:00 2001
From: Joao Morado <joaomorado@gmail.com>
Date: Fri, 3 Jul 2026 15:32:49 +0100
Subject: [PATCH 1/3] Update conda environment

---
 environment.yaml | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/environment.yaml b/environment.yaml
index 668af44..ee0f034 100644
--- a/environment.yaml
+++ b/environment.yaml
@@ -1,30 +1,30 @@
-name: fes-ml-aev
+name: fes-ml
 
 channels:
   - conda-forge
-  - openbiosim/label/emle
+  - openbiosim
 
 dependencies:
   - ambertools
   - compilers
-  - cudatoolkit=11.8
   - eigen
   - loguru
-  - openmm>=8.1
+  - openmm>=8.5
   - openmm-torch
-  - openmm-ml
+  - openmm-ml>=1.7
   - openmmforcefields
   - openff-toolkit
   - openff-interchange
   - nnpops
   - pip
   - pybind11
-  - pytorch=*=*cuda*
+  - pytorch
   - python
   - pyyaml
   - sire
   - torchani
   - pygit2
+  - setuptools<82.0
   - pip:
     - git+https://github.com/chemle/emle-engine.git
     - coloredlogs

From 52a11172ac17498011aabee93ea146bfcf841f58 Mon Sep 17 00:00:00 2001
From: Joao Morado <joaomorado@gmail.com>
Date: Fri, 3 Jul 2026 15:37:53 +0100
Subject: [PATCH 2/3] Improve CUDA installation instructions

---
 README.md | 10 ++++++++--
 1 file changed, 8 insertions(+), 2 deletions(-)

diff --git a/README.md b/README.md
index 7b40bd1..3321e5d 100644
--- a/README.md
+++ b/README.md
@@ -19,19 +19,25 @@ A Python package for running hybrid machine learning/molecular mechanics (ML/MM)
 
 ## Installation
 
-First, create a conda environment with all of the required dependencies:
+First, create a Conda environment with all required dependencies:
 
 ```bash
 conda env create -f environment.yaml
 conda activate fes-ml
 ```
 
-Finally, install `fes-ml` in interactive mode within the activated environment:
+Next, install `fes-ml` in editable mode within the activated environment:
 
 ```bash
 pip install -e .
 ```
 
+For GPU functionality, you must have the appropriate CUDA drivers installed on your host system. On HPC login nodes without GPU drivers, set the `CONDA_OVERRIDE_CUDA` environment variable to the desired CUDA version before creating the Conda environment. For example:
+
+```bash
+CONDA_OVERRIDE_CUDA=12.6 conda env create -f environment.yaml
+```
+
 ## Alchemical Modifications
 
 The following alchemical transformations are supported in fes-ml:

From 36cb79372e17112ece9f448c60b1ab9377fd81c5 Mon Sep 17 00:00:00 2001
From: Joao Morado <joaomorado@gmail.com>
Date: Fri, 10 Jul 2026 12:15:48 +0100
Subject: [PATCH 3/3] Add pymbar as a dependency

---
 environment.yaml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/environment.yaml b/environment.yaml
index ee0f034..1a14ad7 100644
--- a/environment.yaml
+++ b/environment.yaml
@@ -25,6 +25,7 @@ dependencies:
   - torchani
   - pygit2
   - setuptools<82.0
+  - pymbar
   - pip:
     - git+https://github.com/chemle/emle-engine.git
     - coloredlogs