[update] add preprint

README.md

@@ -2,7 +2,7 @@
   <img src="assets/DynaMate.svg" alt="drawing" width="250"/>
   <img src="assets/DynaMate.svg" alt="drawing" width="250"/>
 </p>
 </p>
 
 
-DynaMate is your reliable mate that can run molecular dynamics simulations of protein-ligand and protein-only systems. It is built using LiteLLM and equipt with a collection of tools. Quality checks throughout the pipeline trigger re-tries when something goes wrong, allowing the agent to correct course and save you time on debugging. 
+DynaMate is your reliable mate that can run molecular dynamics simulations of protein-ligand and protein-only systems. It is built using LiteLLM and equipt with a collection of tools. Quality checks throughout the pipeline trigger re-tries when something goes wrong, allowing the agent to correct course and save you time on debugging. You can find our preprint in the `assets` folder.
 
 
 ### Software setup
 ### Software setup
 The tools used by the agent require that you have a local installation of the following software. We provide a Docker image with all dependencies pre-installed (recommended), or you can install everything manually if you prefer
 The tools used by the agent require that you have a local installation of the following software. We provide a Docker image with all dependencies pre-installed (recommended), or you can install everything manually if you prefer

environment.yml

-name: dynagent
+name: dynamate
 channels:
 channels:
   - conda-forge
   - conda-forge
   - defaults
   - defaults

setup.sh

 #!/bin/bash
 #!/bin/bash
 
 
 # load your environment
 # load your environment
-source /home/miniforge3/bin/activate dynagent
+source ~/miniforge3/bin/activate dynagent
 
 
 # Activate GROMACS environment
 # Activate GROMACS environment
 if [ -f /usr/local/gromacs/bin/GMXRC ]; then
 if [ -f /usr/local/gromacs/bin/GMXRC ]; then