Introduction to All-Atom Molecular Dynamics Simulations with Desmond

Tutorial Created with Software Release: 2024-3
Topics: Small Molecule Drug Discovery, Structure Prediction & Target Enablement
Products Used: Desmond, Maestro

Tutorial files

0.8 GB
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:

 

This tutorial guides you through the necessary steps to perform an unrestrained all-atom molecular dynamics (MD) simulation with Desmond. You will prepare the structure of a protein-ligand complex, set up a model system for simulation, run the MD workflow, and perform simple analysis to ascertain the stability and validity of your simulation results. A detailed analysis of the MD results is beyond the scope of this tutorial.

Tutorial Content

  1. Introduction to All-Atom MD Simulations

  1. Creating Projects and Importing Structures

  1. Preparing the Structure of the System

  1. Preparing a Model System and Running the MD Simulation

  1. Analyzing the Stability of the Simulation 

  1. Conclusion and References

  1. Glossary of Terms

1. Introduction to All-Atom MD Simulations

All-atom MD simulations are atomistic models of molecules, where the interactions and motions of atoms are modeled with classical physics, i.e. with a molecular mechanics force field and Newton's law of motion. These simulations generate a time evolution of the system's coordinates in space, which is called a trajectory. This can be interpreted as a molecular movie, whose frames are individual structures of the system and are separated by very short timesteps in the order of femtoseconds. The conditions under which the simulation is performed mimic the real thermodynamic environment and therefore can resemble experimental conditions. For more information on the machinery underlying an MD simulation, click here (YouTube).

By studying the dynamics of a system in a thermodynamic environment, you can investigate processes such as protein folding, protein-protein or protein-ligand interactions, and gain new structural insights for drug discovery and design.

The MD program Desmond and the default OPLS4 force field are part of the Schrödinger suite. It can be used as a standalone tool to unlock structural and dynamical insights of complex molecules, or in conjunction with other programs in the suite, e.g. to sample protein structures prior to performing docking calculations with Glide, or to identify potential binding sites from MD simulation results with SiteMap and Mixed Solvent MD (MxMD). Desmond is also the basis for FEP+, Schrödinger’s free energy perturbation method, which can be used to calculate e.g. accurate binding affinities for in silico drug discovery. Further, Desmond is used in various materials science workflows.

This exploratory tutorial will guide you through the process of setting up and running a simple unrestrained all-atom MD simulation with Desmond through the Maestro graphical user interface (GUI), containing a protein-ligand complex (aldose reductase and zopolrestat) in a box of water and ions. Subsequently, you will perform simple analysis to ascertain the stability and validity of the simulation.

This tutorial does not cover the numerous ways to analyze the results of an MD simulation in detail. For further information on analysis see the Introduction to MD Trajectory Analysis with Desmond tutorial. You can find more information on Desmond in the Desmond User Manual.

2. Creating Projects and Importing Structures

At the start of the session, change the file path to your chosen Working Directorythe location that files are saved in Maestro to make file navigation easier. Each session in 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 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 created, the project is automatically saved each time a change is made.

Structures can be imported from the PDB directly, or from your Working Directorythe location that files are saved using File > Import Structures, and are automatically 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.

  1. Double-click the Maestro icon to start Maestro.

Figure 2-1. Changing the Working Directory via the option in the main window.

  1. Go to File > Change Working Directory.
    • The Change Directory panel opens.
  2. Find and choose the directory you want to use as your working directory.
  3. Pre-generated input and result files are included for running jobs or examining output. Download the .zip file here:https://www.schrodinger.com/sites/default/files/s3/release/current/Tutorials/zip/desmond_intro.zip.
  4. After downloading the zip file, unzip the contents into your Working Directorythe location that files are saved for ease of access throughout the tutorial.

Figure 2-2. Saving the project via the Save Project As dialog box.

  1. Go to File > Save Project As.
    • The Save Project As dialog box opens.
  2. Change the File name to Aldose_Reductase_Intro and
    click     Save.
    • The project is now named Aldose_Reductase_Intro.prj and is saved in your Working Directorythe location that files are saved.

Figure 2-3. Importing the PDB structure via the Get PDB File dialog box.

  1. Go to File > Get PDB.
    • The Get PDB File dialog box opens.
  2. For PDB IDs, type 2DUX.
  3. Click Download.
    • A banner appears confirming the successful import of the structure. 2DUX is added to the Entry Lista simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion and the structure appears in the Workspacethe 3D display area in the center of the main window, where molecular structures are displayed.

Figure 2-4. Applying visualization presets via the Presets button.

  1. Double-click the Presets button
    • The structure is rendered in preset styles and the workspace zooms to the ligand.

3. Preparing the Structure of the System

Structure files obtained from the PDB, vendors, and other sources often lack necessary information for performing modeling-related tasks. Typically, these files are missing hydrogens, have incorrect or missing bond order assignments, charge states, side chain orientation, or are missing whole loop regions. In order to make these structures suitable for MD simulations, the Protein Preparation Workflow is used to resolve common structural issues.

In this section, you will prepare the structure of the aldose reductase system for subsequent MD simulations with Desmond. The default mode of the workflow is the automatic mode, where all settings are made first and all preparation steps are subsequently run in a single job. The other option is the interactive mode, which offers a step-by-step workflow to check and review each step and decision before moving on, so any occurring problem can be addressed.

You will use the default settings for the Protein Preparation Workflow, which work well for this particular system. For other systems a careful inspection of the structural features may be necessary. Please see the Introduction to Structure Preparation and Visualization tutorial, the Protein Preparation Workflow documentation and the Best Practices for Protein Preparation for more in-depth instructions and insights into the use of the Protein Preparation Workflow.

As a preliminary step, visually inspect the protein-ligand complex. Feel free to familiarize yourself with aldose reductase before moving on, e.g. by choosing a visualization style that is most helpful to you. Additionally, you could have a look at the Protein Reliability Report to assess the quality of the structure.

Figure 3-1. Opening the Protein Preparation Workflow panel via the Favorites toolbar.

  1. In the Favorites toolbar, click Protein Preparation or go to Tasks > Browse > Protein Preparation and Refinement > Protein Preparation Workflow.
    • The Protein Preparation Workflow panel opens.

 

 

Figure 3-2. Choosing the included structure from the Workspace for preparation.

  1. In the Specify Protein section of the Preparation Workflow tab, for Use structures from choose Workspace.

Optional: Click Review Structure in the Specify Protein section of the Preparation Workflow tab. Check the Substructures tab for more information on the system contents and the Diagnostics tab for the structural issues of this crystal structure.

Figure 3-3. The three main steps of the Protein Preparation Workflow.

  1. Confirm that Preprocess, Optimize H-bond Assignments and Minimize and Delete Waters are toggled on.

Unlike for docking methods, which usually only require the thorough preparation of a restricted part of the whole complex near the binding pocket, the completeness of the structure is essential for performing MD simulations. This means missing loops and gaps must be reconstructed. The termini must be capped in case the sequence of the structure is not complete, as this would introduce spurious charges at the termini.

Figure 3-4. The Settings for the Minimize and Delete Waters step.

  1. Open the Settings in the Minimize and Delete Waters section.
  2. Make sure that the option Delete waters  Distant from ligands (hets) is not selected.

Deleting the water molecules from the crystal structure, especially those in the binding site, can significantly increase the time needed for equilibration. Nevertheless, crystal waters may not be complete or correct, which can introduce strain in unfilled protein cavities. The solvation can be improved by using WaterMap. Learn more in the Target Analysis with SiteMap and WaterMap tutorial.

Figure 3-5. Naming and running the job.

  1. Change the Job name to proteinprep_2DUX.
  2. Click Run.
    • This job will take ~5 minutes.
    • After completion, a banner appears and the group proteinprep_2DUX-out is added to the Entry Lista simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion.

Optional: Include the prepared structure and check the Diagnostics tab again to see which structural issues have been resolved and which still persist.

4. Preparing and Running the MD Simulation

4.1 Preparing a Model System

The next step after preparing the structure of the protein-ligand complex is to generate a model system for simulation. First, the protein-ligand complex is placed in a box, which is periodically repeated in every dimension (periodic boundary conditions) to simulate infinite dilution and to prevent surface effects. The box is then filled with explicit water molecules and ions, to solvate and neutralize the system. Additional salt ions can be added to resemble certain experimental or biological conditions. If the protein of interest is a membrane protein, a membrane must be set up in this step.

In this section, you will set up the model system for the MD simulation with the System Builder panel. The whole process of system setup can be tedious and often requires a lot of manual work. The system builder automatizes this process and thus significantly reduces the required effort. Setting up a membrane is also possible via the Set Up Membrane Dialog Box, which is directly accessible from the System Builder panel.

Figure 4-1. Choosing the water model in the System Builder panel.

  1. Includethe entry is represented in the Workspace, the circle in the In column is blue the entry 2DUX - prepared.
  2. Go to Tasks > Browse > Classical Simulation > System Setup.
    • The System Builder panel opens in the Solvation tab.
  3. In the Solvent model section select the SPC water model.

The OPLS4 force field has been optimized with the SPC water model, which is a good default choice for simulations with Desmond. For special purposes, other water models can perform better. Further information on water models can be found here. In addition to water, other solvents such as DMSO, ethanol, or octanol have predefined models, but custom solvent models can be employed as well.

Figure 4-2. Choosing the box settings.

  1. In the Boundary conditions section select Orthorhombic as the Box shape.
  2. Select the Show boundary box option.
    • The box into which the complex will be placed is now shown in the Workspacethe 3D display area in the center of the main window, where molecular structures are displayed.
  3. By clicking on Minimize Volume, the complex is centered in the box and the box volume is minimized by reorienting the water molecules.

The choice of box shape is a trade-off between accurately representing the geometry of the system and thus minimizing the number of solvent molecules, and ensuring that the protein-ligand complex is surrounded by a sufficiently large water shell so that it does not interact with copies of itself in neighboring boxes due to periodic boundary conditions (e.g., via rotation).

The orthorhombic box is the default and works well for many systems. However, for highly spherical/globular proteins it may be more efficient to use a more spherical-like box, such as the truncated octahedron or the rhombic dodecahedron.

Figure 4-3. Neutralizing the system with ions.

  1. Switch to the Ions tab of the panel.
  2. Select the option Neutralize by adding … to add the exact amount of Sodium ions (Na+) to neutralize the system. It may be necessary to hit the Recalculate button in order to get the correct amount of ions.

It is usually desirable to have an electrically neutral system for a simulation. Adding counterions makes biological sense because charged molecules are likely to accumulate ions in reality. Additionally, the treatment of long-range electrostatics requires a net-neutral system to avoid artifacts. Thus the correct amount of positive or negative salt ions are added to neutralize the system.

Figure 4-4. Adding a salt concentration to set the ionic strength.

  1. Select the Add salt option and specify a concentration of 0.15 M in the Salt concentration text box.

An additional salt concentration can be specified, e.g. to mimic specific experimental or physiological conditions. For the simulation of most proteins, physiological salt concentrations are reasonable. They can have a huge effect on your simulation, especially for highly charged systems (e.g. RNA/DNA), by weakening the overall electrostatic interactions. However, for some systems there may be no effect at all.

The type of ions for salt concentrations and neutralization can be individually chosen and specific volumes of the system can be excluded. All ions can also be manually placed in the box with the Advanced Ions Placement Dialog Box, instead of having them placed automatically.

Sometimes the protein, ligands or other parts of the system contain coordinated metal ions. To get the coordination correct and stable throughout a simulation you can define zero-order bonds. Learn more here.

Figure 4-5. Naming and running the job.

  1. Change the Job name to desmond_setup_2DUX.
  2. Click Run.
    • This job will take ~2 minutes.
    • After completion, the group desmond_setup_2DUX-out is added to the Entry Lista simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion.  

The OPLS4 force field is the default for Desmond when available and has good parameter coverage over a wide range of chemical space with high accuracy for small molecules, biologics and material science applications. It can be easily reparameterized and extended to novel chemistry as needed, which can be particularly important for applications such as FEP+. For this purpose, the force field can be customized using the Force Field Builder panel.

Figure 4-6. Left: The initially prepared structure. Right: The solvated and neutralized model system.

  1. Once the job is finished and incorporated, Ctrl+click (Cmd+click) to includethe entry is represented in the Workspace, the circle in the In column is blue both 2DUX - prepared entries (before and after system preparation).
  2. Open the Workspace Configuration Panel in the bottom right and select Tile by Entry in the Workspace Layout.
    • Now both entries are displayed in a side by side view for comparison.
  3. Switch the Tile mode off by clicking it again.

4.2 Running the MD Workflow

After setting up the system for an MD simulation, some further steps are necessary to ensure the stability of a subsequent productive simulation. First, an energetic minimization is performed to reconcile the structure with the employed force field. Second, the system must be equilibrated at the desired thermodynamic parameters. Lastly, a production simulation can be performed under the desired conditions for a specified time. This yields a trajectory of configurations, which can then be analyzed.

In Desmond you can combine these steps into one automated and easy to use workflow in the Molecular Dynamics panel. It provides you with the most common simulation controls. You can find more advanced options available via the Advanced Options Dialog Box, e.g. the time step, thermostat, barostat and defining restraints. The default values represent a good balance between accuracy and performance and work for most systems without change.

Figure 4-7. Loading the system from the workspace into the Molecular Dynamics panel.

  1. Make sure only the entry containing the system builder output 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.
  2. Go to Tasks > Browse > Classical Simulation > Molecular Dynamics.
    • The Molecular Dynamics panel opens.
  3. Click Load to load the system from the Workspacethe 3D display area in the center of the main window, where molecular structures are displayed.

Figure 4-8. General options for the productive MD run.

  1. Set parameters for the productive run after equilibration here: Simulation time: 200 ns, Recording interval: 100 ps.
    • The Approximate number of frames is updated automatically.

Figure 4-9. Choosing the ensemble and relaxation protocol.

The NPT or isothermal-isobaric ensemble has a constant number of particles (N), a constant pressure (P) and temperature (T) and represents common experimental conditions.

  1. Choose NPT as the thermodynamic ensemble for the productive run.
  2. Keep the temperature and pressure at standard conditions of 300 (K) and ~1 (bar).

The default protocol for minimization and a series of equilibration steps is used here. It can be changed by writing the protocol to a file and customizing it. More information and the settings of the default protocol can be found here.

 

  1. Select the Relax model system before simulation option to perform an automated minimization and equilibration.

 

The analysis of interactions between the protein and ligand can be automatically included in the MD workflow and is performed after the simulation finishes. This analysis is used by the Simulation Interactions Diagram panel, which you can learn more about in the Introduction to MD Trajectory Analysis with Desmond tutorial.

Here, it is necessary to specify the ligand, because there are two potential ligand molecules present in the system: The zopolrestat molecule, the actual ligand, and the cofactor NADP. The ligand can be defined with the Atom Specification Language (ASL), learn more here.

Figure 4-10. Including an automated interaction analysis in the MD workflow.

  1. In the Analysis section select the option Run interactions analysis when simulation job completes.
  2. For Ligand choose ASL from the option menu and click Define….
    • The Atom Selection Dialog Box opens.

Note: If you opt not to run this analysis now, you can always generate the report later from the Simulation Interactions Diagram panel.

Figure 4-11. Generating an ASL expression for the ligand.

  1. In the Molecule tab, select on the left side Molecule list.
  2. In the Molecule list scroll down to the bottom of the list and select ZST 3.
  3. Click Add.
    • The ASL expression is generated in the ASL field.
  4. Click OK.

Figure 4-12. Running the MD workflow in the Molecular Dynamics panel.

  1. Change the Job name to desmond_md_2DUX.

The MD simulation is now ready to run. Desmond only runs on Linux-based GPUs and in the interest of time, you do not have to run the actual simulation. Pre-generated result files for a 200-ns MD simulation of the system can be found in the zip file you downloaded in the beginning. Feel free to run the simulation if you have access to suitable hardware.

5. Analyzing the Stability of the Simulation

After running an MD simulation, it is important to ascertain the stability and validity of the simulation before proceeding with further analysis. Errors in system preparation, both the preparation of the structure and the model system for simulation, but also inadequate equilibration of the system or errors in the force field can lead to unstable or erroneous simulations.

A visual inspection of the trajectory, as well as energetic and thermodynamic properties of the system, can give a first impression of whether a simulation is stable and sufficiently equilibrated or not. Measured geometric properties such as the root-mean-square displacement (RMSD) can also aid here. In this section, you will analyze pre-generated results of the MD simulation you have set up with the Trajectory Player and the Simulation Quality Analysis panel. The Trajectory Player allows you to play through the frames of a Desmond trajectory, to examine and export them, and to plot properties over the simulation time. The Simulation Quality Analysis panel displays and plots various energetic and thermodynamic quality measures.

Please note that calculations may have been performed with an earlier version of the software and the results may not be exactly the same as those you produced in this tutorial. Especially for methods with a statistical component, such as MD simulations, an exact reproduction of a trajectory and its properties is only possible if the same random seed, software and hardware configuration are used. With sufficient sampling, all properties of the ensemble should be reproducible, while the properties of individual frames and the exact course of a trajectory may differ.

5.1 Trajectory Player

Figure 5-1. Loading the trajectory via the workflow action menu.

  1. Go to File > Import Structures
    • The Import Dialog Box opens.
  2. Navigate to your Working Directorythe location that files are saved, select the file desmond_md_2DUX-out.cms and click Open.
  3. Click Import in the opened window.
    • The group MD: desmond_setup_2DUX is added to the Entry Lista simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion.
  4. Load the trajectory by either double-left-clicking on the small T button in the Title column in the Entry Lista simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion, or by right-clicking on the T button to open the workflow action menu and selecting Load Trajectory.
    • The Trajectory Player opens with the loaded trajectory and the toolbar at the bottom.

Figure 5-2. The Trajectory Player and the Playback Settings.

  1. Click on the Play button in the Play Controls section.
    • The playback through the frames of the trajectory starts. The current frame and corresponding simulation time is indicated in the Frame Controls section.
    • You can pause the playback, jump back to the start and adjust the starting frame and the current frame with the respective sliders in the Frame Control section.
  2. Click on Playback Settings.
    • The Playback Settings Pane opens.
  3. Adjust the playback speed to your liking by clicking on the plus and minus buttons.
  4. Have a look at the trajectory.
  5. Optional: Click on the Beyond binding site option for Hide atoms to focus on the binding pocket.

It is visible that the structure is stable and no severe structural distortions and large scale domain motions occur throughout the simulation. This indicates that the simulation is stable.

You can find more information on further settings of the Trajectory Player here and here, including how to export frames as images or movies. Additionally, you can import Desmond trajectories into PyMOL, to produce publication quality images and movies.

Figure 5-3. Plotting the protein RMSD.

  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 protein via the Quick Select tool.
  2. Click Plot in the Trajectory Player and choose Descriptors (Selected Atoms) > RMSD.
    • After a short time, the Plot Computed Values Over Time Panel opens and your RMSD plot is displayed.

Figure 5-4. The RMSD plotted versus the simulation time.

 

The root-mean-square displacement (RMSD) describes the change in displacement of a selection of atoms for a particular frame with respect to a reference frame, which is typically the first frame. In other words, it is a measure of structural similarity for all frames compared to the starting structure of the simulation. The RMSD can give insights into the structural conformations throughout the simulation. A stabilized RMSD value, which only fluctuates around 1 to 3 Ångstrom around a mean value, confirms the equilibration of the system. Larger changes can indicate insufficient equilibration or conformational changes. Here, the system is equilibrated, no conformational changes occur in the protein.

For more information on the plotting capabilities of the Trajectory Player, see the Plot Computed Values Over Time panel and the Introduction to MD Trajectory Analysis with Desmond tutorial.

5.2 Simulation Quality Analysis

Figure 5-5. The Simulation Quality Analysis panel.

  1. Go to Tasks > Browse > Classical Simulation > Simulation Quality Analysis.
    • The Simulation Quality Analysis panel opens.
  2. To open the energy file of the pre-generated simulation, click Browse, navigate to the file desmond_md_2DUX.ene and click Open.
  3. Click Analyze.
    • The file is read in and the results are shown in the panel.

Figure 5-6. Plotted energies and thermodynamic properties as a function of simulation time.

  1. Click Plot.
    • The values of all properties are plotted along the simulation time and displayed in a new window.
    • The unit for the total and potential energy is kcal/mol. The temperature, pressure and volume are in K, bar and Ų, respectively.

The total and potential energy, the temperature, pressure and volume only fluctuate around an average value, the slope for all properties is zero. This confirms that the equilibration is sufficient and the simulation is stable. Fluctuations on a short time scale around a mean value are expected, but changes over longer time periods would indicate insufficient equilibration or possible instabilities of the simulation.

6. Conclusion and References

In this tutorial you prepared the complex of aldose reductase with the ligand zopolrestat for an unbiased all-atom MD simulation. First, you prepared the crystal structure using the Protein Preparation Workflow. Then, with the System Builder, you set up a model system for an MD simulation by solvating the structure in a box with water, adding a physiological salt concentration, and neutralizing it with sodium ions. The productive MD simulation was part of an automated workflow that included energetic minimization and thermodynamic equilibration prior to the productive MD simulation. Finally, you analyzed the pre-generated MD results for stability and validity of the simulation with the help of the Trajectory Player and the Simulation Quality Analysis panel.

A lot of additional and advanced tools to analyze Desmond MD simulations are available, e.g. the Simulations Interactions Diagram Panel, which graphically displays protein-ligand interactions as well as protein and ligand properties. This is part of the Introduction to MD Trajectory Analysis with Desmond tutorial.

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

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 that files are saved

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