1. Double-click the Materials Science icon
   • (No icon? See Starting Maestro)

Figure 2-1. Change Working Directory option.

2. Go to File > Change Working Directory
3. Find your directory, and click Choose
4. Pre-generated files are included for running jobs or examining output. Download the zip file here: schrodinger.com/sites/default/files/s3/release/current/Tutorials/zip/kmc.zip
5. After downloading the zip file, unzip the contents in your Working Directorythe location where files are saved for ease of access throughout the tutorial

Figure 2-2. Save Project panel.

6. Go to File > Save Project As
7. Change the File name to KMC, click Save
   • The project is now named KMC.prj

Figure 3-1. ADN in the entry list.

1. Go to File > Import Structures
2. Navigate to where you downloaded the provided files (presumably in your Working Directorythe location where files are saved), and choose the ADN.mae file
3. Click Open
   • A new entry is added to the entry lista simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion entitled ADN
4. Select(1) the atoms are chosen in the Workspace. These atoms are referred to as "the selection" or "the atom selection". Workspace operations are performed on the selected atoms. (2) The entry is chosen in the Entry List (and Project Table) and the row for the entry is highlighted. Project operations are performed on all selected entries the ADN entry from the entry lista simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion
   • Please see the Glossary of Terms for definitions of underlined terms such as select(1) the atoms are chosen in the Workspace. These atoms are referred to as "the selection" or "the atom selection". Workspace operations are performed on the selected atoms. (2) The entry is chosen in the Entry List (and Project Table) and the row for the entry is highlighted. Project operations are performed on all selected entries

Figure 3-2. Opening the Conformational Search panel.

We will now perform a conformational search for the ADN molecule. A conformational search allows us to locate low-energy conformers by exploring the conformational landscape of the  molecule and minimizing the resulting structures with a force field.

 

5. Go to Tasks and search for Conformational
6. Choose Conformational Search
   • The Conformational Search panel opens
7. For Solvent, choose none from the option-menu
8. Go to the CSearch tab

Figure 3-3. Setting the CSearch parameters.

The CSearch tab contains the controls for the conformational search. For more information about the options chosen here, visit the thorough help documentation

 

9. For Method, select Low-mode sampling
10. Uncheck Multi-ligand
11. Ensure Perform automatic setup during calculation is checked
12. Check Retain mirror-image conformations
13. Change the Maximum number of steps to 200
14. Change the Job name to mmod_csearch_ADN
15. Adjust the job settings () as needed and click Run.
    • This job takes less than a minute
16. Close the Conformational Search panel
17. Once the job is successfully completed, a new mmod_csearch_ADN-out (6) group, with six entries, is selected(1) the atoms are chosen in the Workspace. These atoms are referred to as "the selection" or "the atom selection". Workspace operations are performed on the selected atoms. (2) The entry is chosen in the Entry List (and Project Table) and the row for the entry is highlighted. Project operations are performed on all selected entries in the entry lista simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion

Figure 3-4. Calculating the Boltzmann Populations for a set of conformers.

Now, let’s calculate the relative weights for each of the ADN conformers using Boltzmann Populations.

 

18. Select(1) the atoms are chosen in the Workspace. These atoms are referred to as "the selection" or "the atom selection". Workspace operations are performed on the selected atoms. (2) The entry is chosen in the Entry List (and Project Table) and the row for the entry is highlighted. Project operations are performed on all selected entries the entry group resulting from the conformational search mmod_csearch_ADN-out (6)
19. Go to Tasks and search for Boltzmann
20. Choose Calculate Boltzmann Populations
    • The Boltzmann Populations panel opens

Figure 3-5. Setting up the Boltzmann Populations calculation.

21. Ensure Use structures from shows Project Table (6 selected entries)
22. For Source energy property, choose Potential Energy-S-OPLS from the option-menu
23. Click Run
    • This job will finish instantaneously and will not add anything to the entry lista simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion. The Boltzmann Population property is added to the Project Tabledisplays the contents of a project and is also an interface for performing operations on selected entries, viewing properties and organizing structures and data
    • Click OK if a message appears
24. Close the Boltzmann Population panel

Figure 3-6. Viewing the Boltzmann Populations in the Project Table.

25. Open the Project Tabledisplays the contents of a project and is also an interface for performing operations on selected entries, viewing properties and organizing structures and data
26. Scroll to find the Boltzmann Population column  

For all six ADN conformers, we see that the Boltzmann population is roughly the same. We can use this information to build a better box of ADN molecules by including an equal number of each conformer. Let’s use the Disordered System Builder panel to create such a cell 

Figure 3-7. Opening the Disordered System Builder panel.

27. Close the Project Tabledisplays the contents of a project and is also an interface for performing operations on selected entries, viewing properties and organizing structures and data
28. Select the entry group resulting from the conformational search mmod_csearch_ADN-out1
29. Go to Tasks > Materials > Structure Builders > Disordered System
    • The Disordered System Builder panel opens

 

Note: For a more in depth explanation of building disordered systems, see the Disordered System Building and Molecular Dynamics Multistage Workflows tutorial

Figure 3-8. Setting the Component parameters.

Here, we want to construct a system of 216 ADN molecules from the conformers and their corresponding Boltzmann weights:

30. For Initial state, choose Amorphous
31. For Number of molecules, input 216
    • A 216 molecule box is reasonable for balancing the computational expense and accuracy of the KMC carrier mobility calculation.
    • The accuracy of the KMC charge mobility calculation can potentially be improved with a larger box, but this involves greater computational expense  

Each ADN component listed in the components table is in order of the conformers selected in the entry lista simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion. To associate the component ratio with the Boltzmann Population for each conformer, we must input quantities manually. Above, we learned that all ADN conformers have roughly the same Boltzmann Population, so in this case we can leave the defaults in place to have an equivalent number of molecules per conformer. If the Boltzmann Populations for conformers were not the same, the value in the % column can be changed to reflect the impact of that conformer in the given system

 

32. For Periodic Boundary Conditions (PBC), select Create new cubic PBC from the option-menu
33. Go to the Cells tab

Figure 3-9. Setting the Cell parameters.

34. We will leave the default options selected in the Cells tab. One cell containing all of the ADN conformers will be created and prepared for a subsequent MD simulation
    • If we were interested in sampling several cells, we could increase the Number of cells of each type
35. Go to the Disorder tab to set the parameters for how the 216 ADN molecules will be packed into a cubic cell

Figure 3-10. Setting the Disorder parameters.

36. Set the Initial density to 0.6
    • Here we set the Initial density to 0.6 g/cm³. In general, it is advised in the building stages to pack the cell to lower density than the expected density. During the MD simulation(s), the box will densify. If during the building stage we attempt to pack the cell to the expected density, the job may either take a long time or crash altogether
37. For Keep constant, choose VdW scale factor
38. Click on Disorder Options
39. Uncheck Steric pack
    • Steric packing attempts to maximize the density of the box which creates a better initial cell, however it also increases the calculation time. Here it is sufficient to build without steric packing as we will follow up with a rigorous MD simulation
40. Click OK

Figure 3-11. Running the Disordered System Builder.

41. Change the Job name to ADN_disordered_system
42. Adjust the job settings () as needed
    • This job requires a CPU host. The job can be completed in 30 minutes on a CPU host with 10 processors
43. If you would like to run the job, click Run. Otherwise, go to File > Import Structures, navigate to the provided tutorial files and Open Section_03 > ADN_cell > ADN_disordered_system_system-out.cms

Figure 3-12. Viewing the disordered system.

44. Once the job is successfully completed or imported, a new ADN_disordered_system_system (1) group, with a single entry titled ADN_disordered_system_all_components_amorphous, is selected(1) the atoms are chosen in the Workspace. These atoms are referred to as "the selection" or "the atom selection". Workspace operations are performed on the selected atoms. (2) The entry is chosen in the Entry List (and Project Table) and the row for the entry is highlighted. Project operations are performed on all selected entries in the entry lista simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion and is includedthe entry is represented in the Workspace, the circle in the In column is blue in the workspacethe 3D display area in the center of the main window, where molecular structures are displayed
45. Close the Disordered System Builder panel

Note that the build is just a starting cell, it is going to be subsequently equilibrated with MD

Figure 4-1. Opening the MD Multistage Workflow panel via the WAM. 

1. Select(1) the atoms are chosen in the Workspace. These atoms are referred to as "the selection" or "the atom selection". Workspace operations are performed on the selected atoms. (2) The entry is chosen in the Entry List (and Project Table) and the row for the entry is highlighted. Project operations are performed on all selected entries the output of the disordered system build, ADN_disordered_system_all_components_amorphous

MD simulations in MS Maestro are performed with the MD Multistage Workflow panel.

2. Use the WAM (workflow action menu) button () to open the MD Multistage Workflow panel
   • Alternatively, access the panel via Tasks > Materials > Classical Mechanics > MD Simulations > MD Multistage Workflow

Figure 4-2. Setting the MD Multistage Workflow stages.

3. Delete () Stage 1
4. Select Append Stages From File at the bottom of the panel
5. From the provided tutorial files, import Section_04 > ADN_MD > eqbr_protocol > equilibration_protocol.msj

Feel free to look through the stages we imported.

Figure 4-3. Running the MD Multistage Workflow calculation.

6. Change the Job name to ADN_multistage_simulation
7. Adjust the job settings () as needed
   • This job requires a GPU host. The job can be completed in about 3 hours on a GPU host
8. If you would like to run the job yourself, click Run. Otherwise, go to File > Import Structures, navigate to the provided tutorial files and Open Section_04 > ADN_MD > ADN_multistage_simulation-out.cms
9. Close the MD Multistage Workflow panel

Figure 4-4. Visualizing the output of the MD simulation.

10. When the job is finished or after importing, select(1) the atoms are chosen in the Workspace. These atoms are referred to as "the selection" or "the atom selection". Workspace operations are performed on the selected atoms. (2) The entry is chosen in the Entry List (and Project Table) and the row for the entry is highlighted. Project operations are performed on all selected entries and includethe entry is represented in the Workspace, the circle in the In column is blue the new ADN_disordered_system_all_components_amorphous entry from the entry lista simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion

 

Note: MD simulations have a number of files associated with the job, for a full description of each file type see the help documentation on Desmond Files

Figure 4-5. Viewing the trajectory.

11. Click on the T button () next to this entry and select Load Trajectory
    • The trajectory is now loaded into the Workspacethe 3D display area in the center of the main window, where molecular structures are displayed
12. Click Play to view the trajectory. Afterwards, close the Trajectory Player ( in the bottom right corner of the workspacethe 3D display area in the center of the main window, where molecular structures are displayed / top right corner of the Trajectory player)
    • To learn more about the Trajectory Player visit the Building, Equilibrating and Analyzing Amorphous Polymers tutorial

Figure 4-6. Loading the trajectory into the MS MD Trajectory Analysis panel.

Finally, we can view bulk properties of the system over the course of the trajectory. We wish to confirm that our system is well-equilibrated before we proceed with the charge mobility calculations:

13. Go to Tasks > Materials > Classical Mechanics > Trajectory Analysis > MS MD Trajectory Analysis
    • The MS MD Trajectory Analysis panel opens
    • Alternatively you can click the WAM button () on the entry to open this panel
14. Click Load from Workspace
    • The Simulation Detail tab fills with information about the MD job and system
15. Go to the Bulk Properties tab

Figure 4-7. Viewing bulk properties of the system.

16. Use the dropdowns to view the various properties as a function of time from the MD stage
    • Click Final 20% to view the last 20% of the trajectory
    • Density and Cohesive energy are shown in the Figure
17. When you are finished, close the MS MD Trajectory Analysis panel  

In the following sections, we will use the equilibrated amorphous ADN cell to calculate the charge mobility properties of the system.

Figure 5-1. Selecting a single frame of the MD simulations.

The KMC Charge Mobility calculation is run on a single frame of an MD simulation. We arbitrarily choose the last frame of the trajectory viewed in the previous section. Any frame can be chosen as long as the structure is well-equilibrated at that point. Let’s now extract a single frame from the trajectory:

 

1. Select(1) the atoms are chosen in the Workspace. These atoms are referred to as "the selection" or "the atom selection". Workspace operations are performed on the selected atoms. (2) The entry is chosen in the Entry List (and Project Table) and the row for the entry is highlighted. Project operations are performed on all selected entries and includethe entry is represented in the Workspace, the circle in the In column is blue the output of the MD simulation in Section 4, ADN_disordered_system_all_components_amorphous
2. Click on the T button () next to this entry and select Load Trajectory
   • The trajectory is now loaded into the Workspacethe 3D display area in the center of the main window, where molecular structures are displayed
3. For Current Frame, enter 1002
   • We choose to export the last frame of our MD simulation
4. Click on Export > Structures
   • The Export Structures panel opens

Figure 5-2. Exporting the current frame.

5. Select Current frame only under Frames
6. Click Export

Figure 5-3. Renaming the exported frame. 

7. Include the entry is represented in the Workspace, the circle in the In column is bluethe single frame and change its name from ADN_disordered_system_all_components_amorphous - Frame 1002 to  ADN_disordered_system_amorphous_Fr1002
8. Close the Trajectory Player ( in the bottom right corner of the workspacethe 3D display area in the center of the main window, where molecular structures are displayed / top right corner of the Trajectory player)

Figure 5-4. Opening the Compute KMC Charge Mobility panel.

We can now use this frame as a basis for our charge hopping parameter calculation.

 

9. Go to Tasks > Materials > Quantum Mechanics > KMC Charge Mobility > New Compute KMC Hopping Parameters
   • The Compute KMC Hopping Parameters panel opens

Figure 5-5. Setting the KMC charge mobility parameters.

10. For Use structures from, select Workspace (included entry)
11. For Charges, select Holes
12. Check Detect identical sites

Figure 5-6. Viewing the neighbor list statistics.

13. In the Neighbor List tab click Update Statistics to see details about the nearest neighbors  

There are a maximum of 16 and a minimum of 7 molecules found as nearest neighbors for the box of 216 ADN molecules. It is best practice to check the minimum and maximum nearest molecules. If the minimum number of nearest neighbors is less than 6, this may indicate that: i) the cutoff radius chosen is too short, or ii) the system is not sufficiently equilibrated, so it contains voids, and some molecules may then trap carriers which would complicate mobility calculations.

Figure 5-8. Running the charge hopping parameter calculation.

14. Change the Job name to charge_hopping_parameters_ADN
15. Adjust the job settings () as needed
    • It is highly suggested to Distribute subjobs across Threads and subjobs to decrease the run time of this job. A good number of CPUs to use is the number of molecules in the box, in this case 216
    • This job requires a CPU host. The job can be completed in ~16 hours on a CPU host with 4 threads and 216 subjobs
16. If you would like to run the job, click Run. Otherwise, go to File > Import Structures, navigate to the provided tutorial files and Open Section_05 > charge_hopping_parameters_ADN > charge_hopping_parameters_ADN-kmc.maegz
17. Close the Compute KMC Charge Mobility panel

Figure 5-9. Restart Hopping Parameter Calculations panel.

18. Once the job is successfully completed or imported, a new charge_hopping_parameter_ADN-kmc (1) group, with a single entry titled ADN_disordered_system_amorphous_Fr1002, is selected(1) the atoms are chosen in the Workspace. These atoms are referred to as "the selection" or "the atom selection". Workspace operations are performed on the selected atoms. (2) The entry is chosen in the Entry List (and Project Table) and the row for the entry is highlighted. Project operations are performed on all selected entries in the entry lista simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion and is includedthe entry is represented in the Workspace, the circle in the In column is blue in the workspacethe 3D display area in the center of the main window, where molecular structures are displayed
    • This entry is the same structure as the frame we extracted from the trajectory in Section 4, but now it has the data from the charge hopping parameter calculation associated with it

 

Since it is such a resource intensive job, there will occasionally be issues with the charge hopping parameter calculation. If the job fails, or completes without successfully calculating all of the charge hopping parameters, we can use the Restart Charge Hopping Parameters panel to troubleshoot.

 

19. Includethe entry is represented in the Workspace, the circle in the In column is blue the result of the calculation, ADN_disordered_system_amorphous_Fr1002
20. Use the WAM (workflow action menu) button () to open the Restart Hopping Parameter Calculations panel
    • Alternatively, access the panel via Tasks > Materials > Quantum Mechanics > KMC Charge Mobility > Restart Hopping Parameter Calculations

We see that 0 sites and pairs are missing data, meaning that the calculation completed successfully. If you ran the calculation yourself and this is not the case, this panel can be used to rerun only the jobs necessary to complete the dataset. For more information about this panel, visit the help documentation

Figure 6-1. Opening the Compute KMC Charge Mobility panel via the WAM.

1. Includethe entry is represented in the Workspace, the circle in the In column is blue the result of the charge hopping parameter calculation, ADN_disordered_system_amorphous_Fr1002
2. Use the WAM (workflow action menu) button () to open the Compute KMC Charge Mobility panel
   • Alternatively, access the panel via Tasks > Materials > Quantum Mechanics > KMC Charge Mobility > Compute KMC Charge Mobility
   • The Compute KMC Charge Mobility panel opens

Figure 6-2. Setting the KMC charge mobility calculation parameters.

3. For Use structures from, Workspace is selected
   • If a different database is to be imported in this option can be changed to Database or File
4. When opening the panel via the WAM, Use database for this structure is checked off by default and the database is loaded in
5. For Charges select the radio-button corresponding to Holes
6. Select Charge mobility via kinetic Monte Carlo
7. Click on Advanced Options  

Figure 6-3. Setting parameters in the KMC tab.

8. Click the KMC tab
9. Enter 1 for Number of carriers
10. For Run time, enter 1000000 KMC Steps

 

Now let’s look at the Electric Field options provided. We want to apply an electric field across the ±x, y and z directions at a range of magnitudes.

 

11. For Axes, select X, Y and Z
12. For Sign, select Positive and Negative
13. The Magnitudes (MV/m) menu allows you to specify the magnitudes of the electric fields to run mobility calculations at.
14. Double-click 1.0 and change it to 0.0
    • We will compare the mobility calculated at 0.0 MV/m to the value predicted by a regression of the data later in this section
15. Click OK  

Figure 6-4. Running the KMC Charge Mobility calculation.

16. Change the Job name to kmc_mobility_ADN
17. Adjust the job settings () as needed
    • Each charge mobility calculation is relatively quick, however we are running many here. It is suggested to Distribute subjobs across CPUs to decrease the run time of this job
    • This job requires a CPU host. The job can be completed in ~25 minutes on a CPU host with 22 CPUs
18. If you would like to run the job, click Run. Otherwise, go to File > Import Structures, navigate to the provided tutorial files and Open Section_06 > kmc_mobility_ADN > kmc_mobility_ADN-kmc.maegz
19. Once the job is successfully completed or imported, a new kmc_mobility_ADN-kmc (1) group, with a single entry titled ADN_disordered_system_amorphous_Fr1002, is selected(1) the atoms are chosen in the Workspace. These atoms are referred to as "the selection" or "the atom selection". Workspace operations are performed on the selected atoms. (2) The entry is chosen in the Entry List (and Project Table) and the row for the entry is highlighted. Project operations are performed on all selected entries in the entry lista simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion and is includedthe entry is represented in the Workspace, the circle in the In column is blue in the workspacethe 3D display area in the center of the main window, where molecular structures are displayed
    • This entry is the same structure as the frame we extracted from the trajectory in Section 4, but now it has the data from the KMC charge mobility calculation associated with it
20. Close the Compute KMC Charge Mobility panel

Figure 6-5. Opening the Plot KMC Charge Mobility panel via the WAM.

We can analyze the output in three ways, with the Plot KMC Charge Mobility, Visualize KMC Charge Transport and Analyze Energetic Disorder panels. Let’s begin with the first:

21. Use the WAM (workflow action menu) button () to open the Plot KMC Charge Mobility panel
    • Alternatively, access the panel via Tasks > Materials > Quantum Mechanics > KMC Charge Mobility > Plot KMC Charge Mobility
    • The Plot KMC Charge Mobility panel opens

Figure 6-6. Viewing the KMC charge mobility plot.

Here we are viewing a plot of the log of the mobility as a function of the square root of the electric field. We can also view the drift velocity of the charge. For ADN, we expect to see the charge mobility increase with the field as is observed here. The default data series is the average mobility over the electric fields in the ±x, y and z directions. To look at the charge mobility along a field of particular sign or direction, we can uncheck the Average for fields with different signs and Average for fields along different axes.

 

Additionally, if relevant, the calculated KMC zero field mobility can be compared to the extrapolated zero field mobility. For more information about the capabilities of this panel, visit the help documentation

Figure 6-7. Opening the Visualize KMC Charge Transport panel via the WAM.

Let’s move on to the Visualize KMC Charge Transport panel:

22. Use the WAM (workflow action menu) button () to open the Visualize KMC Charge Transport panel
    • Alternatively, access the panel via Tasks > Materials > Quantum Mechanics > KMC Charge Mobility > Visualize KMC Charge Transport
    • The Visualize KMC Charge Transport panel opens

Figure 6-8. Visualizing molecules in the workspace by occupancy.

For this example, we will arbitrarily choose to view the charge transport for an electric field of 100.0 MV/m along the -X axis.

23. For Database, select Hole, Field -X = 100 MV/m
24. Uncheck Coarse-grained representation
25. Check Visualize molecules by and select Occupancy
    • Occupancy tells us the fraction of total simulation time in which a site is charged. The slider range, 0.000 to 0.609 tells us that some molecules are never charged and others are charged over two-third of the simulation time
26. Change the value of the left-hand side of the slider to 0.080
    • Only two molecules remain in the workspacethe 3D display area in the center of the main window, where molecular structures are displayed. These molecules are visited most often by the charge

Figure 6-9. Visualizing the coarse-grained representation by occupancy.

27. We can visualize the same information for the coarse-grained representation. Uncheck Visualize molecules by
28. Check Coarse-grained representation
29. Check Sites and select Occupancy
30. Change the value of the left-hand side of the slider to 0.080
    • Again, only two molecules remain in the workspacethe 3D display area in the center of the main window, where molecular structures are displayed as expected. This is the site the charge visits most often
31. Check Color by
32. Choose Site energy from the option menu and choose Blue-Red for the Color map
    • The sites in Blue have low energies while those colored red have high energies
33. Ensure that you are still visualizing the highest occupancy site as done in Steps 27 & 28

 

The highest occupancy site is also the lowest energy site. Conversely, if you use the slider to look at the sites with 0 occupancy, you will see that those molecules are colored dark red, indicating high energy values.

Figure 6-10. Viewing the Analyze Energetic Disorder panel.

The Analyze Energetic Disorder panel facilitates plotting histograms of the variation in Site energy, Coupling integral and Reorganization energy (hop on/off) for a given system.

34. Use the WAM (workflow action menu) button () to open the Analyze Energetic Disorder panel
    • Alternatively, access the panel via Tasks > Materials > Quantum Mechanics > KMC Charge Mobility > Analyze Energetic Disorder

 

Proceed to explore other properties from the Plot KMC Charge Mobility, Visualize KMC Charge Transport and Analyze Energetic Disorder panels on your own depending on your interests