MBO(N)D

5       Command Summary--Insight

MBO(N)D is accessed in the Insight environment by choosing MBOND from the Module pulldown (which is accessed by clicking the MSI logo). The MBOND module contains several pulldowns (in addition to the core pulldowns on the top menu bar), which appear on the lower menu bar. They are: Bodies, Modes, SetUp, MBOND_Run, Background_Job, and Forcefield. Each pulldown gives access to several related commands. The SetUp pulldown, for example, contains a set of commands used in setting up an MBO(N)D calculation: Dynamics, NonBond, and Files.

What the commands in these pulldowns do is summarized briefly below. For more detailed explanations of individual commands, refer to the on-line help facility (by clicking the help icon, which is the button containing a question mark, on the left side of the main Insight window). For information on how to use these commands, see Chapter 4, Methodology--Insight.

Bodies pulldown

The Bodies/Get command is used to read in sets of atoms from a file to define bodies. The file contains only the SUBSTR section of MBO(N)D input with the atom selections described using the CHARMm SELECT BYNUm commands.

The Bodies/Put command is used to write a set of bodies to a file. The file contains only the SUBSTR section of MBO(N)D input with the atom selections described using the CHARMm SELECT BYNUm commands.

The Bodies/Define command is used to specify sets of atoms that are to be treated as bodies. Within the Define command the Molecule Spec parameter box and the Property Name and Substructure Method value-aids are powerful tools that allow you to substructure your molecule using a wide variety of methods.Use Molecule Spec to select large portions of the molecule, then select Property and Substructure Method options to further define bodies.

The Bodies/Edit command is used to modify the atoms and colors that constitute the body. Atoms may be added or deleted and are described in the same way as in the Bodies/Define command.

The Bodies/Delete command is used to delete a single body or set of bodies from the model.

The Bodies/Color command is used to color the atoms within a body using the color specified when the body was defined. This is useful for visualizing the atoms in particular bodies when the model coloring has been modified. You can choose to color atoms which have not been assigned to a body by selecting Subset/NOT_IN_BODY from the Parameters window.

The Bodies/List command is used to output information about previously defined bodies. This includes the atoms, color, and modes associated with each body.

Modes pulldown

The Modes/Load command is used to associate a set of modes from a user specified file with a body. These modes are then loaded during subsequent MBO(N)D dynamics simulations.

The Modes/Generate command is used to create a set of modes for the specified body. This starts an MBO(N)D simulation that only generates modes and does not include dynamics.

The Modes/Animate command is used to visualize a mode for a body. This creates a temporary animation of the body using the mode as a displacement vector from the nominal coordinates stored in the specified modes file. This is useful for visualizing the modes before associating them for the simulation.

SetUp pulldown

The SetUp/Minimize command is used to set up a minimization run.

The SetUp/Dynamics command is used to modify the parameters for the various dynamics stages, including heating, equilibration, and simulation.

The SetUp/NonBond command is used to modify the parameters used in calculating nonbond interactions during a simulation.

The SetUp/Files command is used to control how often various information is output, including coordinates, velocities, energies, and restart information.

The SetUp/Parameter_Mode command is used to control runs in PSF or RTF mode and to select parameter files for RTF mode.

The SetUp/MTS_Integrator command is used to modify parameters used in the MBO(N)D multiple time step integrator.

MBOND_Run pulldown

The MBOND_Run/Minimize command is used to start a minimization job.

The MBOND_Run/MBOND_Run command is used to start an MBO(N)D dynamics run.

Background_Job pulldown

The Background_Job/Control_Bkgd_Job command allows you to coordinate running background jobs by detaching selected background jobs from or attaching them to the current Insight session. In addition, this command allows you to specify the interval for invoking a task specific to a particular background job for processing its output.

The Background_Job/Completion_Status command allows you to monitor and evaluate the completion status of one or all background jobs. In addition, this command can be used to look up the meaning of a return status code.

The Background_Job/Kill_Bkgd_Job command is used to terminate execution of a background job that was submitted during the current Insight session.