Hybrid Monte Carlo Panel

Run hybrid Monte Carlo simulations to search nearby conformational space, through a sequence of short, high-temperature molecular dynamics simulations followed by minimization. The high temperature MD simulation allows the structure to move between minima on the potential energy surface. New conformations are accepted or rejected based on standard Monte Carlo criteria. The result is either the lowest-energy conformations or all of the conformations produced from each MD/minimization step.

Only structures that are accepted by the Monte Carlo criteria are returned. If there are steps in the job where no structures are accepted, these steps do not return a final structure. Consequently, the actual number of structures returned at the end of the job  may be smaller than the number of steps set for the job.

To open this panel, click the Tasks button and browse to Protein Preparation and Refinement → Hybrid Monte Carlo.

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 prime Command Help and prime—Build and Refine Protein Structures.

  • Features
  • Additional Resources

Hybrid Monte Carlo Panel Features

Use structures from option menu

Choose the structure source for the current task.

  • Project Table (selected entries)—Use the entries that are currently selected in the Project Table.
  • Workspace (included entry)—Use the entry that is currently included in the Workspace. Only one entry must be included in the Workspace.
  • File—Use the specified file. When this option is selected, the File name text box and Browse button are displayed.
File name text box and Browse button

Enter the file name in this text box, or click Browse and navigate to the file. The name of the file you selected is displayed in the text box.

Solvation model option menu

Choose a continuum solvation model for the refinement. The choices are:

  • VSGB—Use the variable-dielectric generalized Born model, which incorporates residue-dependent effects. The solvent is water.
  • Vacuum—Do not include solvation.
  • Chloroform—Use chloroform as the solvent, modeled with the Surface Generalized Born (SGB) method.
Force field option menu

Choose the force field for the current task. The choices are OPLS_2005 and OPLS4. The default is OPLS4 if it is available, otherwise it is OPLS_2005, unless you set the default in the Force Field settings section of the Preferences Panel.

Use customized version option

Use your customized version of the OPLS4 force field, rather than the standard version in the distribution. Only available when you choose OPLS4 from the Force field option menu and you have the appropriate license. This option is set by default to the value of the Use custom parameters by default option in the Preferences panel, under Jobs - Force field, when the current panel is opened. The default directory for the customized version can also be specified as a preference, in the same location.

If the customized version is missing or invalid, the text of this option turns orange and an orange warning icon is displayed to the right, with a tooltip about the problem.

Parameter set button

Select the set of custom parameters for the OPLS4 force field. Opens the Set Custom Parameters Location Dialog Box. Only available when you choose OPLS4 from the Force field option menu and you have the appropriate license.

Atoms for refinement picking tools

Select the atoms for refinement using the standard picking tools.

Constraints button

Open the Hybrid Monte Carlo - Constraints Dialog Box, to set up distance (atom-pair) and Cartesian (initial position) constraints.

Options button

Open the Hybrid Monte Carlo - Options Dialog Box to set up options, including use of an implicit membrane and crystal symmetry, the solvent dielectric constant, temperature, number of steps, and output.

Job toolbar

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

The Job Settings button opens the Hybrid Monte Carlo - 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.

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