merged from main into experiments

README.md

@@ -1,12 +1,12 @@
-MDAgent is a LLM-agent based toolset for Molecular Dynamics.
+MDCrow is a LLM-agent based toolset for Molecular Dynamics.
 It's built using Langchain and uses a collection of tools to set up and execute molecular dynamics simulations, particularly in OpenMM.
 
 
 ## Environment Setup
 To use the OpenMM features in the agent, please set up a conda environment, following these steps.
 ```
-conda env create -n mdagent -f environment.yaml
-conda activate mdagent
+conda env create -n mdcrow -f environment.yaml
+conda activate mdcrow
 ```
 
 If you already have a conda environment, you can install dependencies before you activate it with the following step.
@@ -16,7 +16,7 @@ If you already have a conda environment, you can install dependencies before you
 
 ## Installation
 ```
-pip install git+https://github.com/ur-whitelab/md-agent.git
+pip install git+https://github.com/ur-whitelab/MDCrow.git
 ```
 
 ## Usage
@@ -25,14 +25,14 @@ We recommend setting up api keys in a .env file. You can use the provided .env.e
 1. Copy the `.env.example` file and rename it to `.env`: `cp .env.example .env`
 2. Replace the placeholder values in `.env` with your actual keys
 
-You can ask MDAgent to conduct molecular dynamics tasks using OpenAI's GPT model
+You can ask MDCrow to conduct molecular dynamics tasks using OpenAI's GPT model
 ```
-from mdagent import MDAgent
+from mdcrow import MDCrow
 
-agent = MDAgent(model="gpt-3.5-turbo")
+agent = MDCrow(model="gpt-3.5-turbo")
 agent.run("Simulate protein 1ZNI at 300 K for 0.1 ps and calculate the RMSD over time.")
 ```
-Note: to distinguish Together models from the rest, you'll need to add "together\" prefix in model flag, such as `agent = MDAgent(model="together/meta-llama/Meta-Llama-3.1-70B-Instruct-Turbo")`
+Note: to distinguish Together models from the rest, you'll need to add "together\" prefix in model flag, such as `agent = MDCrow(model="together/meta-llama/Meta-Llama-3.1-70B-Instruct-Turbo")`
 
 ## LLM Providers
 By default, we support LLMs through OpenAI API. However, feel free to use other LLM providers. Make sure to install the necessary package for it. Here's list of packages required for alternative LLM providers we support:
@@ -43,6 +43,6 @@ By default, we support LLMs through OpenAI API. However, feel free to use other
 
 ## Contributing
 
-We welcome contributions to MDAgent! If you're interested in contributing to the project, please check out our [Contributor's Guide](CONTRIBUTING.md) for detailed instructions on getting started, feature development, and the pull request process.
+We welcome contributions to MDCrow! If you're interested in contributing to the project, please check out our [Contributor's Guide](CONTRIBUTING.md) for detailed instructions on getting started, feature development, and the pull request process.
 
-We value and appreciate all contributions to MDAgent.
+We value and appreciate all contributions to MDCrow.