Molecular Dynamics Panel

In this panel you can set up and restart Desmond molecular dynamics simulations.

To open this panel: click the Tasks button and browse to Classical Simulation → Molecular Dynamics.

  • Using
  • Features
  • Additional Resources

Using the Molecular Dynamics Panel

Molecular dynamics jobs simulate the Newtonian dynamics of the model system, producing a trajectory of the particles' coordinates, velocities, and energies, on which statistical analyses can be performed to derive properties of interest about the model system. The molecular dynamics task performs a single MD simulation under the chosen ensemble condition for a given model system, generating simulation data for post-simulation analyses. The model system should be prepared with the System Builder Panel.

The Molecular Dynamics panel is designed to make setting up jobs as easy as possible. The main panel provides the most common simulation controls, while the Advanced Options dialog box provides access to a larger range of parameters. The default values represent a good balance between accuracy and performance and work for most jobs without change, but can be changed as needed. Model systems that contain membranes are detected automatically, and the defaults are set appropriately.

To run a molecular dynamics simulation job:

  1. Specify the model system, either by loading it from the Maestro Workspace or importing it from a file.

  2. Choose Molecular dynamics from the Simulation task option menu.

  3. Adjust the simulation parameters as necessary.

    For parameters that are not available in the main panel, open the Advanced Options dialog box.

    In particular, select Relax model system before simulation or Relax membrane model system before simulation if the model system has not been relaxed before. Usually, if the model system was just created from the System Builder panel, it needs to be relaxed; if the model system has been relaxed before, it does not need to be relaxed again.

  4. Click the Settings button , set the job parameters in the Job Settings dialog box, and click Run to run the job.

To restart an interrupted molecular dynamics job:

  1. Import the checkpoint file generated by the interrupted simulation.

    The default name of this file is jobname.cpt.

    When the checkpoint file is successfully imported, the Desmond panel enters a read-only state, in which most of the controls are set by the information read and cannot be changed.

  2. Adjust the total simulation time if necessary.

  3. Click the Settings button , set the job parameters in the Job Settings dialog box, and click Run to run the job.

To write out the input file and a script for running the job from the command line, click the arrow next to the Settings button and choose Write. For information on command usage and options, see multisim Command Help.

Molecular Dynamics Panel Features

Model system section

In this section, you select the model system that you will use for the simulation. A valid model system must contain both the coordinates of the particles and the force field parameters. A file of a valid model system normally has the .cms extension. You can use the System Builder Panel to prepare the model system for any structure that you have. If you want to build an amorphous structure from scratch, you can use the Disordered System Builder Panel to create a model system.

The option menu offers two choices for the source of the model system:

  • Load from Workspace—Load the model system from the Workspace. When you choose this option, the Load button is displayed to the right of the menu. Click this button to load the model system.

  • Import from file—Import the model system from a file. When you choose this option, a text box and Browse button are displayed to the right of the menu. You can enter the name of the file in the text box, or click Browse and navigate to the file.

    You can choose to import a model system file (.cms) or a checkpoint file (.cpt).

    If you import a model system file, it must contain a model system that has already been prepared. When the file is imported, a message about the system is displayed below the option menu.

    If you import a checkpoint file, most of the panel controls are unavailable. The purpose of the checkpoint file is to restart an interrupted simulation, so the parameters of the simulation cannot be altered. You can change the total simulation time, and then start the job.

Simulation section

In this section, you make the basic settings for the MD simulation.

Simulation time text boxes

Specify the total time of the simulation, in ns, in the total text box. Changing the total simulation time changes the trajectory recording interval, to maintain a maximum of 1000 frames in the trajectory.

The elapsed text box displays the amount of time the simulation has already run, if you are restarting a simulation. For new simulations it should contain zero. This text box cannot be edited.

Recording interval text boxes

Specify the recording interval for the energy and the trajectory, in ps, in the energy and trajectory text boxes. Values entered in these text boxes are rounded to an integer multiple of the far time step size. By default, the far time step size is 0.006 ps. This time step size is set in the Integration tab of the Molecular Dynamics - Advanced Options Dialog Box, in the RESPA integrator section. If you adjust the trajectory recording interval, the number of frames is updated.

Approximate number of frames text box

Specify the approximate number of frames in the trajectory. This value is coupled with the recording interval for the trajectory and the simulation time: the number of frames times the trajectory recording interval is the total simulation time. If you adjust the number of frames, the recording interval is modified.

Ensemble class option menu

Choose the ensemble class from this option menu. The following classes are available:

  • NVE—constant particle number (N), volume (V) and energy (E). This class represents the microcanonical ensemble.
  • NVT—constant particle number (N), volume (V) and temperature (T). This class represents the canonical ensemble.
  • NPT—constant particle number (N), pressure (P) and temperature (T). This class is an isothermal-isobaric ensemble, the common experimental conditions.
  • NPAT—constant particle number (N), pressure (P), lateral surface area (A), and temperature (T). This class is an isothermal-isobaric ensemble with constant normal pressure and lateral surface area i.e. the pressure coupling is nonisotropic.
  • NPγT—constant particle number (N), pressure (P), lateral surface tension (γ), and temperature (T). This class represents an isothermal-isobaric ensemble with constant normal pressure and lateral surface tension, i.e. the pressure coupling is nonisotropic.

The last two ensembles are often used for membrane-containing systems. Fixing the surface area or surface tension helps to ensure that the simulation box does not deform significantly in the plane of the membrane while the pressure is applied normal to the membrane surface.

Temperature text box

Specify the temperature to be used, in kelvin. Not available for the NVE ensemble class.

Pressure text box

Specify the pressure to be used, in bar. Not available for the NVE and NVT ensemble classes.

Surface tension text box

Specify the surface tension to be used, in bar angstroms. Only available for the NPγT ensemble class.

Relax model system before simulation option

When selected, a series of minimizations and short molecular dynamics simulations are performed to relax the model system before performing the simulation you set up (see Relaxing a Model System). If the system contains a membrane, the option text reads Relax membrane model system before simulation, and relaxation protocols suitable for a membrane-bound system are used (see Relaxing a Membrane-Containing Model System).

Normally, this option is needed only for model systems that have just been prepared with the System Builder Panel or the Disordered System Builder Panel, and have not been relaxed. This option is selected by default for a new simulation, but is deselected and unavailable if you are starting from a checkpoint file.

Relaxation protocol text box and Browse button

Specifiy a custom protocol to be used for the relaxation. You can specify a protocol by clicking Browse and selecting the appropriate .msj file for the relaxation. The text box shows the name of the file you selected.

Advanced Options button

Opens the Molecular Dynamics - Advanced Options dialog box, in which you can control many more of the detailed settings for the simulation than are available in the Molecular Dynamics panel.

Analysis section

Run the interactions analysis that is used by the Simulation Interactions Diagram Panel. When the job finishes, you can open this panel to examine the interactions by clicking the View Simulation Analysis link in the banner that is displayed.

Run interactions analysis when simulation completes option

Select this option to run the analysis of protein and ligand interactions after the simulation, and return the .eaf file, which contains the analysis results.

Protein and Ligand option menus and tools

Specify the parts of the protein and the ligand on which to perform the analysis. The option menu and associated tools are the same for both the protein and the ligand.

  • Auto—use the automatic detection of the protein or ligand. This choice uses the protein or ligand ASL aliases. See Ligand Detection Preferences for information on automatic ligand detection.

  • None—do not analyze the protein or ligand (whichever is relevant). This allows you to just analyze the protein or just analyze the ligand.

  • ASL—define the protein or ligand atoms to analyze by selection of atoms. Click the Define button to open the Atom Selection Dialog Box to make the choice, or enter an ASL expression in the text box. The text box is populated when you close the Atom Selection Dialog Box, and you can edit the resultant expression. See Atom Specification Language for more information on ASL.

Job toolbar

Manage job submission and settings. See Job Toolbar for a description of this toolbar.

The Job Settings button opens the Molecular Dynamics - Job Settings Dialog Box, where you can make settings for running the job.

Status bar

The status bar displays information about the current job settings and status for the panel. The settings includes the job name, task name and task settings (if any), number of subjobs (if any) and the host name and job incorporation setting. The job status can include messages about job start, job completion and incorporation.

Use the Reset button to reset the panel to its default settings and clear any data from the panel. You can also reset the panel from the Job toolbar.

The status bar also contains the Help button , which opens the help topic for the panel in your browser. If the panel is used by one or more tutorials, hovering over the Help button displays a button, which you can click to display a list of tutorials (or you can right-click the Help button instead). Choosing a tutorial opens the tutorial topic.

Tutorials

Related Topics