CheckAdaptLig Flow

Contents:

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

Usage

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