Reactions Discovery
*******************

ReaxFF Reaction discovery

Starting with AMS2024, the Amsterdam Modeling Suite contains a
Reactions Discovery workflow for finding possible (side) reactions
from a set of reactant molecules.

See also:

  * Reactions Discovery Documentation

  * Reactions Discovery Python example

In this tutorial, you will predict some possible reactions for MEA
(monoethanolamine) in CO₂ and H₂O, using a ReaxFF force field.


Set up and run Reactions Discovery
==================================

   **1.** Start **AMSinput**
   **2.** Select the Workflows panel: [image: ADFPanel][image] **→** [image: WorkflowsPanel][image]

   [image]

   **3.** Set **Task** to **Reactions Discovery**
   **4.** Click the [image: MoreBtn][image] next to the Task, or switch to the **Model → Reactions Discovery** panel.

   [image]

The main Reactions Discovery input panel contains the most important
input settings.

For the NanoReactor, the most important number to modify is the
**Minimum volume fraction**, which controls how strong the reactor is.
For details, see the Reactions Discovery documentation.

In this tutorial, we will leave all settings at the default values,
but it's a good idea to experiment with different numbers.

   Click the [image: MoreBtn][image] next to **Build System**. This brings you to the RD System panel.
   Set **Number of atoms** to "200" (default)
   Set **Density** to "0.9" g/cm³.
   Tick the **Equilibration** checkbox

   Click the [image: AddButton][image] next to **Molecule**
   Enter **SMILES**: "O"   (this is water)
   Enter **Relative mole fraction**: "1.0"

   Click the [image: AddButton][image] next to **Molecule**
   Enter **SMILES**: "NCCO"  (this is MEA)
   Enter **Relative mole fraction**: "2.0"

   Click the [image: AddButton][image] next to **Molecule**
   Enter **SMILES**: "O=C=O"  (this is CO₂)
   Enter **Relative mole fraction**: "3.0"

   [image]

When the job runs, this will build the initial system with
approximately 200 atoms at a density of 0.9 g/cm³ with the specified
relative mole fractions. Feel free to change the number of atoms or
density to see how it affects the resulting simulation.

   Switch back to main Reactions Discovery panel: **Model → Reactions Discovery**

Here you can see that the **Engine** is set to **ReaxFF 1**. In this
tutorial, we will use ReaxFF, but you can also change it to a
different engine. Keep in mind that the simulations can be quite
computationally expensive, so it's best to use a fast compute engine.

   Click on the **ReaxFF 1** panel **at the bottom of the AMSinput window**.
   Click the folder icon next to **ForceField**, and select **CHON-2019.ff**

   [image]

Then save and run the job:

   **File → Save**
   **File → Run**

The calculation will take a few minutes to finish.


View the Reactions Discovery Results
====================================

Wait until the calculation has finished.

   Switch to AMSjobs: **SCM → Jobs**
   Select the job
   Open the results in AMSmovie: **SCM → Movie**

   [image]

This shows all molecules that were generated, which can be quite many.

Let's filter on only the stable products:

   In AMSmovie, select **Reactions Discovery → Filter Categories → Products**

   [image]

This shows the list of products in order of formation likelihood.

Note:

  Your results may be different from those shown here, as the
  reactions discovery relies on molecular dynamics simulations.


View the individual MD simulations
==================================

It is always helpful to inspect the individual MD simulations to see
if the reactor is too aggressive or not aggressive enough.

   In AMSmovie, select **File → Open** and browse to one of the "mdsim_0", "mdsim_1", etc. directories inside the "jobname.results" directory, and select the **ams.rkf** file to open.
   This shows the nanoreactor simulation.

   [image]

Tip:

  The displayed energy is the total energy including the kinetic and
  restraint energies. Use **Graph → Engine Energy** to view the
  ReaxFF-calculated potential energy without restraints.

   [image]

See the Reactions Discovery Frequently Asked Questions for tips on how
to tune the parameters of the simulation
