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CheckAdaptLig flow is a tool that helps the user to investigate an adaptive-like simulation (Adaptive or AdaptiveGoal). The flow will inspect the trajectory providing general information about the simulations and attempts to automatically build a Markov State Model (MSM). Furthermore, several analysis of the model are performed to provide useful information:

• lag time used for the MSM
• number of macrostates created
• evaluation of the macrostate membership
• plot of the implied timescales
• figures of the macrostates generated

The flow summarizes all the information in HTML, which can be open and read with any web browser

## Example¶

Get the data for running the CheckAdaptLig flow examples here.

Analysis of a Adaptive Goal of D3-Receptor and Eticlopride

To analyze the example case, which uses D3 receptor as protein and Eticlopride as ligand, one can use the following command:

aceflow CheckAdaptLig --inputtrjs checkadaptlig/data --inputtopo checkadaptlig/Structures/structure.pdb --outdir test_checkadaptlig --metric distances


Finally, one can visualize the results by opening the HTML report using:

google-chrome test_checkadaptlig/reportCheckAdaptLig_quick.html