diff --git a/README.md b/README.md index 5d3909ac..5560eaf6 100644 --- a/README.md +++ b/README.md @@ -12,7 +12,7 @@ OpenMMDL @ Molecular Design Lab -Interface to OpenMM for easy setup of molecular dynamic simulations of +Interface to **OpenMM** for easy setup of molecular dynamic simulations of protein-ligand complexes http://openmmdl.readthedocs.io/ @@ -28,7 +28,7 @@ Open a new terminal and clone this repository #### Install all required dependencies in a separate environment -OpenMMDL is written in python 3.10 and uses several packages, which can +**OpenMMDL** is written in Python 3.10 and uses several packages, which can be easily installed on a separate environment using conda (we recommend using miniconda): @@ -43,24 +43,23 @@ After installation, activate the conda environment: pip install . -## OpenMMDL-Setup +## OpenMMDL Setup -OpenMMDL-Setup will setup an MD simulation for OpenMM (i.e. create all -the needed files for running the simulation) +**OpenMMDL Setup** will allow you to prepare the files needed to perform an protein-ligand complex MD simulation with **OpenMM**. ### Usage -Start the setup process by executing the command: +Start **OpenMMDL Setup** by executing the command: openmmdl_setup -The setup interface is displayed through a web browser, but it is still +The **OpenMMDL Setup** interface is displayed through a web browser, but it is still a single-user desktop application, not a web application. It should automatically open a web browser displaying the user interface. If that does not happen for any reason, open a browser and point it to the address displayed in the console window (e.g. http://127.0.0.1:5000). -Download the processed PDB File and python script, which serve as input -for the simulation script. +Download the processed PDB file and Python script, which will serve as input +for the **OpenMMDL Simulation** script. ## OpenMMDL-Simulation