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 input and results files are included for running jobs or examining output. Download the zip file here: schrodinger.com/sites/default/files/s3/release/current/Tutorials/zip/free_volume.zip
5. After downloading the zip file, unzip the contents in your Working Directory 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 free_volume_tutorial, click Save
   • The project is now named free_volume_tutorial.prj

Figure 2-3. The entry list and workspace after importing.

In Section 3 of this tutorial, we will analyze a Zn-MOF structure. In Section 4, we will analyze a polymer trajectory. Let’s import these structures now:

8. Go to File > Import Structures
9. Import Zn_MOF.mae
10. Click Open
    • Zn_MOF is added to the entry list
11. Import multistage_simulation_PS > multistage_simulation_PS-out.cms
12. Click Open
    • polymer_builder_PS_system is added to the entry list

Figure 3-1. Parameterizing the Free Volume Analysis panel.

1. With the Zn_MOF entry selected and included, go to Tasks > Materials > Tools > Free Volume Calculations
   • The Free Volume Analysis panel opens
2. Maintain the defaults for Use grid spacings and Probe radius
   • The calculation (by default) will be run at four different grid spacings, 1.00 Å, 0.75 Å, 0.50 Å and 0.25 Å. Evaluating over a range allows us to assess convergence
   • The probe radius is used to determine whether a grid point is a void or not; the default here is good. If you want to use multiple radii, you can use the output of one analysis to run another with a different probe radius
3. Change the Job name to free_volume_MOF
4. Click Run
   • This job takes ~5 minutes on a 12 CPU host. Adjust your job settings as needed.

Figure 3-2. Accessing the results via the WAM.

When the job is complete, a banner appears to indicate that the output has been incorporated. A new entry group entitled free_volume_MOF-freevolume (1) is added to the entry list with one entry titled Zn_MOF

5. Select and include the new Zn_MOF entry
6. Use the Workflow Action Menu (WAM) button in the entry list and click on Free Volume Results
   • The Free Volume Analysis Viewer panel opens

Note: Alternatively, access the Free Volume Analysis Viewer via Tasks > Materials > Tools > Free Volume Results

Figure 3-3. Radius, spacing and void statistics.

The Probe radius and Grid spacing can be selected from the dropdowns at the top of the panel. We used 1.40 Å for probe radius and four different grid spacings. We will analyze the grid spacing of 0.25 Å

Also at the top of the results panel, you can see several void statistics, including the number of total voids, the free volume overall percent as well as the mean and median void size.

Figure 3-4. Distribution tab.

In the Distribution tab, a histogram titled Void Size Distribution of fractional volume versus volume-equivalent sphere radius is shown. In the case of this structure, essentially all of the void volume is the largest cavity of the MOF.  

 

Adjusting the Number of bins, allows adjusting the size of the groupings in which the void sizes are grouped.

Figure 3-5. Display the voids.

The voids can be visualized in the workspace.

7. Click Display next to Number of voids to display
   • Be patient, as the voids can take a moment to load in the workspacethe 3D display area in the center of the main window, where molecular structures are displayed
   • The filter can be used to define the size of voids to display

The voids are displayed as surfaces (the surface occupies the negative space). You can see details about the various voids, or hide/display specific voids using the surface button () in the entry list

8. Hide the surfaces by clicking on the surface button  () in the entry lista simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion and choosing Hide All

Figure 3-6. Void location plot.

Return to the Free Volume Analysis Viewer panel. We will discuss the Cumulative tab in detail in Section 4, though in general this tab can be useful in MOF applications for determining the pore-limiting diameter.

9. Go to the Location tab
   • The location of the voids in a cross-section is shown
   • A plane is shown in the workspace that indicates the location of the current cross section
   • Use the View along dropdown and the green arrows to toggle the plane to various locations

The voids are shown as colored blobs, with color indicating a specific void; as stated before, the main void here is all one interconnected entity, thus the blobs are all the same color

Note: double-clicking on a blob within the plot will result in that void being displayed in the workspace as a surface

Figure 3-7. Convergence plot.

10. Go to the Convergence tab
    • The convergence of the free volume as a function of the grid spacing is shown. In this case, the grid spacing of 1.00 Å is sufficient

Note: Smaller grid sizes allow for more accurate results, but also result in significantly more expensive calculations. Thus, the convergence plot can be used to evaluate the necessary grid spacing for an accurate free volume analysis

For a complete summary of all aspects of the Free Volume Analysis Viewer panel, visit the help documentation

11. Close the Free Volume Analysis Viewer panel

Figure 4-1. Polystyrene system in the workspace.

1. Select and include polymer_builder_PS_system from the entry list (imported in Section 2)

Note: For practice building amorphous polymers, see the Building, Equilibrating and Analyzing Amorphous Polymers tutorial

Figure 4-2. Parameterizing the Free Volume Analysis panel.

2. Go to Tasks > Materials > Tools > Free Volume Calculations
   • The Free Volume Analysis panel opens

Because this system includes a trajectory, the Free Volume Analysis panel allows for the analysis to performed over some or all of the trajectory

3. Check Analyze trajectory
4. Click Trajectory Range and set the filter to 900-1000 (9.00 - 10.00 ns) with a Step size of 10. Click OK
   • Here we are only looking at some of the trajectory to simplify the calculation
   • A range can be specified, as well as a step size
5. Maintain the defaults for Use grid spacings and Probe radius
   • In practice, computational resources can be conserved by running multiple grid spacings on one frame from the trajectory to ensure convergence, and then running the free volume job at the max sufficient grid spacing post-convergence
6. Change the Job name to free_volume_polymer
7. This job takes ~15 hours on a CPU host. If you do not wish to run the job, rather than proceeding to Step 7, import amorphous_polypolystyrene-12-out.cms from the provided tutorial files (in the Section_04 > free_volume_polymer directory), then continue to Step 8.
8. Otherwise, adjust your job settings as needed and click Run

Figure 4-3. Accessing the results via the WAM.

9. Select and include the new polymer_builder_PS_system from the entry list
10. Use the Workflow Action Menu (WAM) button in the entry list and click on Free Volume Results

Note: Alternatively, access the Free Volume Analysis Viewer via Tasks > Materials > Tools > Free Volume Results

Figure 4-4. Void size distribution for one frame.

11. Click Load Data from Workspace

The Free Volume Analysis Viewer opens on the Distribution tab with data for just the last frame of the trajectory showing.

 

As before, the Probe radius and Grid spacing can be adjusted according to the input settings.

 

Adjusting the Number of bins, allows adjusting the size of the groupings in which the void sizes are grouped.

Figure 4-5. Void size distribution for a range of frames.

12. Adjust the Number of frames slider to 7
    • The Void Size Distribution graph updates to now include the data for 11 equally spaced frames (every 0.10 ns from 4.0 to 5.0 ns)

 

Note: Voids can be displayed in the workspace as we observed in Section 3. In general with trajectory analysis, it is advisable to Precalculate All Voids before viewing voids to facilitate the loading of the surfaces in the workspace without significant delay.

As before, the Location tab can be used to visualize the location of the voids in a cross-section. Additionally, the Convergence can be used to verify that the grid spacing employed was sufficient.