diff --git a/networks/Preparing AlchemicalNetworks.ipynb b/networks/Preparing AlchemicalNetworks.ipynb index 06c0087..b415cb8 100644 --- a/networks/Preparing AlchemicalNetworks.ipynb +++ b/networks/Preparing AlchemicalNetworks.ipynb @@ -602,7 +602,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.10.10" + "version": "3.10.11" } }, "nbformat": 4, diff --git a/rbfe_tutorial/cli_tutorial.md b/rbfe_tutorial/cli_tutorial.md index a030e32..1b8fc84 100644 --- a/rbfe_tutorial/cli_tutorial.md +++ b/rbfe_tutorial/cli_tutorial.md @@ -1,16 +1,16 @@ # Relative Free Energies with the OpenFE CLI This tutorial will show how to use the OpenFE command line interface to get -free energies -- with no Python at all! This will work for simple setups, you +free energies -- with no Python at all! This will work for simple setups, but you may need to use the Python interface for more complicated setups. The entire process of running the campaign of simulations is split into 3 -stages; each of which corresponds to a CLI command: +stages, each of which corresponds to a CLI command: 1. Setting up the necessary files to describe each of the individual - simulations to run. -2. Running the simulations. -3. Gathering the results of separate simulations into a single table. + simulations to run +2. Running the simulations +3. Gathering the results of separate simulations into a single table To work through this tutorial, start out with a fresh directory. You can download the tutorial materials (including this file) using the command: @@ -40,7 +40,7 @@ To run the command, we do the following: the option `-M tyk2_ligands.sdf`. You can also use `-M` with a directory, and it will load all molecules found in any SDF or MOL2 file in that directory. * Pass a PDB of the protein target (TYK2) with `-p tyk2_protein.pdb`. - * Instruct `openfe` to ouput files into a directory called `network_setup` + * Instruct `openfe` to output files into a directory called `network_setup` with the `-o network_setup` option. ```bash @@ -101,10 +101,10 @@ how these simulation are set up: minimum distance of 1.2 nm from the solute to the edge of the box. 4. The protocol used is OpenFE's OpenMM-based Hybrid Topology RFE protocol, with [default settings](https://docs.openfree.energy/en/stable/reference/api/openmm_rfe.html#protocol-settings). -## Customize you Campaign Setup +## Customize your campaign setup -OpenFE contains many different options and methods for setting up a calculation campaign. -The options can be easily accessed and modified with providing a settings +OpenFE contains many different options and methods for setting up a simulation campaign. +The options can be easily accessed and modified by providing a settings file in the `.yaml` format. Let's assume you want to exchange the LOMAP atom mapper with the Kartograf atom mapper and the Minimal Spanning Tree @@ -123,7 +123,7 @@ network: openfe plan-rbfe-network -M tyk2_ligands.sdf -p tyk2_protein.pdb -o network_setup -s settings.yaml ``` -3. The output of the CLI program will now reflect the made changes: +3. The output of the CLI program will now reflect the changes made: ```text RBFE-NETWORK PLANNER @@ -236,7 +236,7 @@ files are the actual results of a simulation. Other files that are generated during the simulation (such as detailed simulation information) have been replaced by empty files to keep the size smaller. The structure looks something like this: - +openfe ```text