Dynamic Relaxed Coordinate Scans

Tutorial Created with Software Release: 2024-4
Topics: Catalysis & Reactivity, Organic Electronics, Polymeric Materials, Thin Film Processing
Methodology: Molecular Quantum Mechanics
Products Used: Jaguar, Jaguar, MS Maestro, Maestro

Tutorial files

15 MB
This tutorial is written for use with a 3-button mouse with a scroll wheel.
Words found in the Glossary of Terms are shown like this: Workspacethe 3D display area in the center of the main window, where molecular structures are displayed

 

Tip: You can hover over a glossary term to display its definition. You can click on an image to expand it in the page.
Abstract:

 

In this tutorial, we will learn to use dynamic relaxed coordinate scans for exploring potential energy surfaces.

Tutorial Content

  1. Introduction to Dynamic Variable Relaxed Coordinate Scans

  1. Creating Projects and Importing Structures

  1. Comparing Scan Types for a One-Dimensional Nucleophilic Attack

  1. Running a Dynamic Variable Relaxed Scan for the Beckmann Rearrangement

  1. Running a Dynamic Variable Relaxed Scan for Cyclohexane Chair-Boat Transition

  1. Conclusion and References

  1. Glossary of Terms

1. Introduction to Dynamic Variable Relaxed Coordinate Scans

Exploration of the potential energy surface (PES) is a common task in molecular modeling. A typical exercise is to calculate the change of energy along a particular molecular coordinate (i.e. a distance, angle or dihedral), while at the same time keeping the rest of the coordinates frozen or letting them relax (rigid and relaxed coordinate scans, respectively). These two scan types are discussed in the  Rigid and Relaxed Coordinate Scans tutorial. In this tutorial, we will be discussing two types of relaxed coordinate scans: fixed variable and dynamic variable scans.

dynamic variable relaxed coordinate scan

Schrödinger’s quantum mechanics (QM) engine, Jaguar is capable of performing constrained geometry optimizations using fixed constraints or dynamically constrained variables. In this tutorial, we will refer to these as fixed variables and dynamic variables, respectively. When a fixed variable is specified for a particular coordinate (e.g., bond length, bond angle, or dihedral angle), the initial geometry is modified in order to set the coordinate to the desired value. Then, during the optimization, the rest of the geometry is relaxed. While intuitive and simple to implement, the fixed variable approach can potentially lead to steric clashing or extreme strain at the start of the geometry optimization. Furthermore, it is highly complicated for systems such as rings where the optimal coordinate set is non-obvious.

Dynamic variables allow the structure to slowly adjust the geometry to the constraint. The geometry starts with its initial coordinates, and then is slowly pulled to minimize the error in the dynamic constraint. This allows us to avoid bad starting in positions with steric clashing and more easily incorporate multiple constraints. We can use dynamic variables within coordinate scans, i.e., “dynamic scan” to scan over coordinates that are inaccessible due to the limitations of fixed variables.

Jaguar automates the procedure for running fixed variable and dynamic variable relaxed coordinate scans. In a scan, you specify the values of the coordinates, and Jaguar performs geometry optimization calculations on the molecule at those coordinate values or on an initial geometry targeting the specified coordinates.

Coordinate scans can contribute to our understanding of different molecular processes, for example, we can see what the energy landscape looks like for a particular parameter (e.g. is this bond very rigid? does this dihedral have a high degree of freedom?) and through that we can understand features such as rotational barriers and conformational landscapes. By understanding bond breaking or bond forming processes, we can generate initial guesses for transition states. To learn more about how coordinate scans can facilitate finding transition states, visit the Rigid and Relaxed Coordinate Scans tutorial. Additionally, optimal bond lengths, bond angles and dihedrals identified from coordinate scans can be used to parameterize a force field.

In this tutorial, we will study three systems using coordinate scans; (1) in Section 3 we will compare fixed variable and dynamic variable scans for studying a nucleophilic attack, (2) in Section 4 we will run a dynamic variable scan for the Beckmann rearrangement, and (3) in Section 5 we will run a two-dimensional dynamic variable scan to study the conformations of cyclohexane.

2. Creating Projects and Importing Structures

At the start of the session, change the file path to your chosen Working Directorythe location where files are saved in MS Maestro to make file navigation easier. Each session in MS Maestro begins with a default Scratch Projecta temporary project in which work is not saved, closing a scratch project removes all current work and begins a new scratch project, which is not saved. A MS Maestro project stores all your data and has a .prj extension. A project may contain numerous entries corresponding to imported structures, as well as the output of modeling-related tasks. Once a project is saved, the project is automatically saved each time a change is made.

Structures can be built in MS Maestro or can be imported using File > Import Structures (or drag-and-dropped), and are added to the Entry Lista simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion and 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. The Entry Lista simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion is located to the left of the Workspacethe 3D display area in the center of the main window, where molecular structures are displayed. 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 can be accessed by Ctrl+T (Cmd+T) or Window > Project Table if you would like to see an expanded view of your project data.

OR

  1. Double-click the Maestro or Materials Science icon

Note: This Jaguar workflow can be performed in Maestro or Materials Science Maestro. Use whichever interface you are comfortable with or typically use for your projects.

Figure 2-1. Change Working Directory option.

  1. Go to File > Change Working Directory
  2. Find your directory, and click Choose
  3. 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/dynamic_scans.zip
  4. 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.

  1. Go to File > Save Project As
  2. Change the File name to dynamic_scans_tutorial, click Save
    • The project is now named dynamic_scans_tutorial.prj

Figure 2-3. Viewing the imported molecules.

  1. Go to File > Import Structures
  2. Navigate to where you downloaded the tutorial files (presumably in your working directory), and choose input_molecules.mae. Click Open
    • A new entry group titled input_molecules (3) appears in the entry lista simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion. This input contains the structures needed for the exercises in this tutorial

If you are interested in building and optimizing similar structures yourself, feel free to do so. For a refresher on using the 2D Sketcher or importing structures, see the Introduction to Maestro for Materials Science tutorial. For how to perform geometry optimization, see the Introduction to Geometry Optimizations, Functionals and Basis Sets tutorial.

3. Comparing Scan Types for a One-Dimensional Nucleophilic Attack

In this section, we will use the Jaguar - Relaxed Coordinate Scan panel to perform two relaxed coordinate scans on the C-O bond length in an SN2-type of nucleophilic attack of a methoxide ion on ethylene oxide. We will run a relaxed coordinate scan first treating the C-O bond length as a fixed variable and then as a dynamic variable and compare the results. If you are interested in reviewing relaxed coordinate scans with fixed variables, please see the Rigid and Relaxed Coordinate Scans tutorial.

Arrow pushing mechanism for the nucleophilic attack of a methoxide ion on ethylene oxide

Figure 3-1. Opening the relaxed coordinate scan panel.

  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 methoxide_ethylene_oxide in the entry lista simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion
  2. Go to Tasks > Browse All > Jaguar > Relaxed Coordinate Scan
    • The Jaguar - Relaxed Coordinate Scan panel opens
    • The level of theory and basis set shown in the Input tab are set to the defaults which are sufficient for this example

Figure 3-2. Viewing the Solvation tab.

  1. Go to the Solvation tab
    • It is practical to include implicit solvation in our coordinate scans for this system
  2. From the drop-down menu, select PCM for the Solvent model
  3. Set the Solvent to methanol

Figure 3-3. Viewing the Scan tab.

  1. Go to the Scan tab
    • Here we can specify the parameters for our coordinate scan

Let’s understand the settings and capabilities of the Jaguar - Relaxed Coordinate Scan panel a bit more:

  • With respect to the coordinates
    • The Type gives you the choice between scanning about Distances, Angles, Dihedrals, and Coordinates
    • You can Pick the coordinate of interest interactively in the workspacethe 3D display area in the center of the main window, where molecular structures are displayed by selecting either Atoms or Bonds
    • You can choose up to five coordinates of interest
  • The Selected coordinate section allows you to ​​set the range of the scan and the spacing of the points along the scan coordinate for the coordinate that is selected in the table
  • If you are interested in seeing more examples of running coordinate scans, visit the Rigid and Relaxed Coordinate Scans tutorial or see the help documentation for a complete summary of the parameters shown in the panel

Figure 3-4. Adding the coordinate of interest.

  1. From the Type drop-down menu under Add new coordinate, select Distance
  2. Check Pick and ensure Atoms is selected from the menu
    • We will indicate the atoms that make up the bond length of interest in the workspacethe 3D display area in the center of the main window, where molecular structures are displayed
  3. Arrange the panel and (MS) Maestro window in a way that you can see the structure in the workspacethe 3D display area in the center of the main window, where molecular structures are displayed and the panel simultaneously
  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 following atoms in the workspacethe 3D display area in the center of the main window, where molecular structures are displayed as shown in the Figure: O and C
    • The distance we wish to probe is shown in the workspace with a blue dashed line

Figure 3-5. Setting the scan parameters.

  1. Keep Fixed Value checked
    • We will first run a fixed variable coordinate scan for the system
  2. For the Selected coordinate, enter 1.38 for the Starting value
  3. For the Final value, enter 3    
  4. For the Increment, enter 0.16
    • The scan points will be 0.16 Å apart
    • The Total number of structures to be calculated updates to 11

 

Note: Starting geometries for the dynamic scan could alternatively be generated from previously optimized geometries. When run this way, each scan point's starting geometry is (exactly) initialized to the previous point's converged geometry. This is slightly different from Consecutive Relaxed Scans which use fixed constraints where the previous point's converged geometry is modified to satisfy the value of the scan coordinate before optimization.

Figure 3-6. Running the fixed variable relaxed coordinate scan.

  1. Change the Job name to jag_sn2_relaxed_scan
  2. Adjust the job settings () as needed. This job requires a CPU host. This job can be parallelized across resources as there are 11 short, independent jobs to be run. The job can be completed in 45 minutes on 11 CPUs
  3. 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 03 > jag_sn2_relaxed_scan > jag_sn2_relaxed_scan_scan > jag_sn2_relaxed_scan.01.mae
  4. Do not close the Jaguar - Relaxed Coordinate Scan panel as we will continue with the current settings in the next step

Figure 3-7. Running the dynamic variable relaxed coordinate scan.

  1. Without changing any other parameters in the panel, uncheck Fixed Value
    • We are now ready to run a dynamic variable coordinate scan on our system
  2. Change the Job name to jag_sn2_dynamic_scan
  3. Adjust the job settings () as needed. This job requires a CPU host. This job can be parallelized across resources as there are 11 short, independent jobs to be run. The job can be completed in one hour on 11 CPUs
  4. 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 03 > jag_sn2_dynamic_scan > jag_sn2_dynamic_scan_scan > jag_sn2_dynamic_scan.01.mae
  5. Close the Jaguar - Relaxed Coordinate Scan panel

Figure 3-8. Visualizing the output.

  1. When the jobs are 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 first entry from the jag_sn2_relaxed_scan.01 (11) entry group
    • Feel free to visualize the output system in the workspacethe 3D display area in the center of the main window, where molecular structures are displayed
    • We can analyze the coordinate scan by visualizing the different entries in this group
    • Feel free to visualize the output from the dynamic relaxed scan as well

Figure 3-9. Updating bonds. Structures are tiled here for clarity.

In visualizing the results of the coordinate scans, you may notice some bonds that are unusually short or long as an artifact of the calculation. The bond lengths depicted in the workspace are arbitrary and do not have significance. This is purely visual, but can be easily amended using the Update Bonds feature.

 

  1. Includethe entry is represented in the Workspace, the circle in the In column is blue all structures you would like to recalculate bonds for using Shift + Click
  2. Click the Workspace Configuration Panel ()
  3. Click Update Bonds

 

The bonds in the structures in the workspace are now updated. At any point in this tutorial, feel free to make this visual adjustment to outputs of coordinate scans. 

Figure 3-10. Opening the Plot Coordinate Scan Results panel.

Now, let’s analyze our coordinate scan more quantitatively. We will use the Plot Coordinate Scan Results panel to look at the relative energies for each step of our coordinate scans:

 

  1. For the jag_sn2_relaxed_scan.01 (11) entry group, use the WAM button () to open the Plot Energy Across Scan Coordinates panel

Figure 3-11. Plotting the results for the fixed variable scan.

If you used the WAM button, feel free to skip steps 23 and 24 as the results of your relaxed scan will be loaded into the panel automatically.

 

  1. If you opened the panel from the tasks menu, click Load Results
  2. Navigate to the Section 03 > jag_sn2_relaxed_scan > jag_sn2_relaxed_scan_scan > jag_sn2_relaxed_scan.grd file and click Open
    • The relative energy (kcal/mol) for each optimized structure is plotted as a function of the coordinate
    • The energy units can be adjusted using the Energy Options menu

 

Repeat the above steps to plot coordinate scan results for the jag_sn2_dynamic_scan.01 (11) entry group.

Let’s combine the qualitative and quantitative information about the fixed variable and dynamic variable relaxed coordinate scans for the C–O bond length to learn more:

fixed variable coordinate scan

dynamic variable coordinate scan

To begin, let’s discuss the initial geometries generated by both types of coordinate scans. In the fixed variable scan the initial geometry varies at every scan step, but some initial geometries may not be good starting points for performing a geometry optimization. Note that at the last few scan steps the nucleophile is very close to ethylene oxide, but the ring’s geometry remains unchanged, which is not physically meaningful.

In contrast, the dynamic scan starts from identical initial geometries but sets different target distances between the carbon atom of ethylene oxide and the oxygen atom of the nucleophile. As a result, the corresponding geometry optimizations start from physically more acceptable geometries, in which the ethylene oxide ring gradually relaxes as the nucleophile approaches to satisfy the target distance.

The final results of the fixed and dynamic scans in this example are very similar, both in terms of geometries and energies. A C–O bond length of 1.38 Å is clearly energetically most favorable. So in this case it does not matter which scan we perform - fixed or dynamic.

4. Running a Dynamic Variable Relaxed Scan for the Beckmann Rearrangement

In this section, we will use the Jaguar - Relaxed Coordinate Scan panel to perform a dynamic relaxed coordinate scan for the well-known Beckmann rearrangement. Here we would like to scan the distance between the attacking carbon atom and the nitrogen atom, essentially simulating the formation of the new C–N bond. In this case a scan with a fixed variable scan cannot be performed, as the scan variable is a part of the ring. The fixed variable algorithm does not know how to construct the initial geometries because it is unclear how the uninvolved atoms in the ring should move. A dynamic scan is the solution. The initial geometry at every scan step is the same, as in the previous example, but the target changes. All coordinates are updated dynamically in the course of geometry optimization by using Lagrange multipliers.

Arrow pushing mechanism for the Beckmann rearrangement.

Figure 4-1. Opening the relaxed coordinate scan panel.

  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 beckmann_rearrangement in the entry lista simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion
    • This structure has been geometry optimized at the B3LYP-D3 level of theory using the 6-31G+* basis set
  2. Go to Tasks > Browse All > Jaguar > Relaxed Coordinate Scan
    • The Jaguar - Relaxed Coordinate Scan panel opens
    • The level of theory and basis set shown in the Input tab are set to the defaults which are sufficient for this example

Figure 4-2. Viewing the Solvation tab.

  1. Go to the Solvation tab
    • It is practical to include implicit solvation in our coordinate scans for this system
  2. From the drop-down menu, select PCM for the Solvent model
  3. Set the Solvent to methanol

Figure 4-3. Adding the coordinate of interest.

  1. Go to the Scan tab
    • Here we can specify the parameters for our coordinate scan
  2. From the Type drop-down menu under Add new coordinate, select Distance
  3. Check Pick and ensure Atoms is selected from the menu
    • We will indicate the atoms that make up the distance of interest in the workspacethe 3D display area in the center of the main window, where molecular structures are displayed
  4. Arrange the panel and (MS) Maestro window in a way that you can see the structure in the workspacethe 3D display area in the center of the main window, where molecular structures are displayed and the panel simultaneously
  5. 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 following atoms in the workspacethe 3D display area in the center of the main window, where molecular structures are displayed as shown in the Figure: N and C
    • The distance we wish to probe is shown in the workspace with a blue dashed line

Figure 4-4. Setting the scan parameters.

  1. Uncheck Fixed Value
  2. For the Selected coordinate, enter 1.48 for the Starting value
  3. For the Final value, enter 2.45
  4. For the Increment, enter 0.065
    • The scan points will be 0.065 Å apart
    • The Total number of structures to be calculated updates to 15

Figure 4-5. Running the coordinate scan.

  1. Change the Job name to jag_beckmann_rearrangement
  2. Adjust the job settings () as needed. This job requires a CPU host. This job can be parallelized across resources as there are 15 short, independent jobs to be run. The job can be completed in 3 hours on 12 CPUs
  3. 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 > jag_beckmann_rearrangement > jag_beckmann_rearrangement_scan > jag_beckmann_rearrangement.01.mae
  4. Close the Jaguar - Relaxed Coordinate Scan panel

 

Note: For a quick estimation, feel free to run coordinate scans with less scan points. For a more precise traversal of the potential energy surface, feel free to increase the number of scan points.

Figure 4-6. Visualizing the output.

  1. When the jobs are 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 first entry from the jag_beckmann_rearrangement.01 (15) entry group
    • Feel free to visualize the output system in the workspacethe 3D display area in the center of the main window, where molecular structures are displayed
    • We can analyze the coordinate scan by visualizing the different entries in this group

Figure 4-7. Opening the Plot Coordinate Scan Results panel.

Now, let’s analyze our coordinate scan more quantitatively. We will use the Plot Coordinate Scan Results panel to look at the relative energies for each step of our coordinate scan:

 

  1. For the jag_beckmann_rearrangement.01 (15) entry group, use the WAM button () to open the Plot Energy Across Scan Coordinates panel

Figure 4-8. Plotting the results.

If you used the WAM button, feel free to skip the steps below as the results of your Relaxed scan will be loaded into the panel automatically.

 

  1. If you opened the panel from the tasks menu, click Load Results
  2. Navigate to the Section 04 > jag_beckmann_rearrangement > jag_beckmann_rearrangement_scan > jag_beckmann_rearrangement.grd file and click Open
    • The relative energy (kcal/mol) for each optimized structure is plotted as a function of the coordinate
    • The energy units can be adjusted using the Energy Options menu

Let’s combine the qualitative and quantitative information about the dynamic variable coordinate scan for the for the C–N bond length to learn more:

The dynamic variable relaxed scan successfully captured the ring expansion as a part of the Beckmann rearrangement. As seen in the GIF above, as the dynamic variable scan progresses, the new C–N bond and a water molecule are formed. There is a large dip in energy when the water molecule dissociates from the structure leading to a more stable form. The high energy structure found in the scan could be used as a guess for a transition state search. For a smoother plot, more scan points would have to be defined.

5. Running a Dynamic Variable Relaxed Scan for Cyclohexane Chair-Boat Transition

In this section, we will use the Jaguar - Relaxed Coordinate Scan panel to perform a dynamic variable relaxed coordinate scan for cyclohexane. Specifically, we will scan two dihedral angles defined by the atoms C2-C3-C4-C5 and C5-C6-C1-C2 shown below. By scanning these two angles it is possible to transform from the boat conformation to the chair conformation. In this particular example, we are using dynamic constraints to scan over coordinates within a ring structure – which would not be possible with a fixed constraint scan.

Cyclohexane with carbon atoms numbered.

Figure 5-1. Applying element and atom number labels.

  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 cyclohexane in the entry lista simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion
    • This structure has been geometry optimized at the B3LYP-D3 level of theory using the 6-31G+* basis set
  2. Go to the Style () menu
  3. Click Apply Labels
  4. Click Element + Atom Number
    • The atoms in cyclohexane are now labeled with their element type and atom number. This will allow us to identify our dihedral angles of interest easily

Figure 5-2. Opening the relaxed coordinate scan panel.

  1. Go to Tasks > Browse All > Jaguar > Relaxed Coordinate Scan
    • The Jaguar - Relaxed Coordinate Scan panel opens
    • The level of theory and basis set shown in the Input tab are set to the defaults which are sufficient for this example
    • You may need to reset () the panel to clear out the solvent selection from the last calculation, we will not be simulating a solvent here
  2. Go to the Scan tab

Figure 5-3. Adding the first coordinate of interest.

  1. From the Type drop-down menu under Add new coordinate, select Dihedral
  2. Check Pick and ensure Atoms is selected from the menu
    • We will indicate the atoms that make up the dihedral of interest in the workspacethe 3D display area in the center of the main window, where molecular structures are displayed
  3. Arrange the panel and (MS) Maestro window in a way that you can see the structure in the workspacethe 3D display area in the center of the main window, where molecular structures are displayed and the panel simultaneously
  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 following atoms in the workspacethe 3D display area in the center of the main window, where molecular structures are displayed as shown in the Figure: C5, C6, C1, and C2
    • Select the atoms in the exact order lister as it is significant for defining the correct dihedral angle
    • The first dihedral angle we wish to rotate about is shown in the workspace with a blue arrow

Figure 5-4. Setting the scan parameters.

  1. Uncheck Fixed Value
  2. For the Selected coordinate, enter 0 for the Starting value
  3. For the Final value, enter 55
    • We choose this final value as it is close to the potential energy surface minimum, the chair conformation
  4. For the Increment, enter 5.0
    • The scan points will be 5 degrees apart
    • The Total number of structures to be calculated updates to 12

Figure 5-5. Adding the second coordinate of interest.

We can scan over up to five coordinates using this panel. In this example, we are interested in studying the chair to boat conformational change in cyclohexane, which involves rotating about two dihedral angles. Now, let’s select the second dihedral angle we are interested in studying:

 

  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 following atoms in the workspacethe 3D display area in the center of the main window, where molecular structures are displayed as shown in the Figure: C2, C3, C4, and C5
    • Select the atoms in the exact order lister as it is significant for defining the correct dihedral angle
    • The second dihedral angle we wish to rotate about is shown in the workspace with a blue arrow

Figure 5-6. Setting the scan parameters.

  1. Uncheck Fixed Value
  2. For the Selected coordinate, enter -55 for the Starting value
  3. For the Final value, enter 0.0
  4. For the Increment, enter 5.0
    • The scan points will be 5 degrees apart
    • The Total number of structures to be calculated updates to 144

Figure 5-7. Running the coordinate scan.

  1. Change the Job name to jag_cyclohexane_scan
  2. Adjust the job settings () as needed. This job requires a CPU host. This job can be parallelized across resources as there are 144 short, independent jobs to be run. The job can be completed in 3 hours on 12 CPUs
  3. 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 05 > jag_cyclohexane_scan > jag_cyclohexane_scan_scan > jag_cyclohexane_scan.01.mae
  4. Close the Jaguar - Relaxed Coordinate Scan panel

Figure 5-8. Visualizing the output.

  1. When the jobs are 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 first entry from the jag_cyclohexane_scan.01 (144) entry group
    • Feel free to visualize the output system in the workspacethe 3D display area in the center of the main window, where molecular structures are displayed
    • We can analyze the coordinate scan by visualizing the different entries in this group

Figure 5-9. Opening the Plot Coordinate Scan Results panel.

Now, let’s analyze our coordinate scan more quantitatively. We will use the Plot Coordinate Scan Results panel to look at the relative energies for each step of our coordinate scan:

 

  1. For the jag_cyclohexane_scan.01 (144) entry group, use the WAM button () to open the Plot Energy Across Scan Coordinates panel
    • Alternatively, go to Tasks > Materials > Tools > More Tools > Plot Coordinate Scan
    • The Plot Coordinate Scan Results panel opens
    • If you do not use the WAM to open the panel, please import the jag_cyclohexane_scan.grd file as done in previous sections

 

 

In this case, the use of dynamically constrained variables has enabled us to perform a two-dimensional scan over dihedral angles that exist in cyclohexane's ring configuration. As desired, we are able to calculate the PES of cyclohexane which contains both chair and boat conformations. You can click on the coordinates of interest in the contour plot and see the geometry associated with that scan point in the workspace. Additionally, the contour plot provides us with an estimate for the barrier height between the two conformations and shows the expected half-chair conformation at the maxima between the two (as shown in the GIF).

6. Conclusion and References

In this tutorial, we learned how to calculate and analyze the results of dynamic variable relaxed coordinate scans using Jaguar.

For further learning:

For introductory content, focused on navigating the Schrödinger Materials Science interface, an Introduction to Materials Science Maestro tutorial is available. Please visit the materials science training website for access to 70+ tutorials. For scientific inquiries or technical troubleshooting, submit a ticket to our Technical Support Scientists at help@schrodinger.com.

For self-paced, asynchronous, online courses in Materials Science modeling, including access to Schrödinger software, please visit the Schrödinger Online Learning portal on our website.

If you are interested in running Jaguar calculations from the command line, please visit the documentation for example files and guidance.

For some related practice, proceed to explore other relevant tutorials:

7. Glossary of Terms

Entry List - a simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion

Included - the entry is represented in the Workspace, the circle in the In column is blue

Project Table - displays the contents of a project and is also an interface for performing operations on selected entries, viewing properties, and organizing structures and data

Recent actions - This is a list of your recent actions, which you can use to reopen a panel, displayed below the Browse row. (Right-click to delete.)

Scratch Project - a temporary project in which work is not saved, closing a scratch project removes all current work and begins a new scratch project

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

Working Directory - the location where files are saved

Workspace - the 3D display area in the center of the main window, where molecular structures are displayed