Advanced MD Options Dialog Box

This dialog box provides access to advanced molecular dynamics options for control of the simulation or the minimization, such as the frequency of data output, thermostat and barostat parameters, and so on.

  • Features
  • Additional Resources

Advanced MD Options Dialog Box Features

Note: The features available in the dialog box and the default values depend on the application from which it is opened. This topic lists all available features.

Thermostat section

Specify settings for the thermostat in this section.

Method option menu

The thermostat method is automatically selected based on the input structure, from Nose-Hoover chain for all-atom systems, Langevin for Martini coarse-grained systems, or DPD for DPD systems.

The thermostat method and the barostat method are coupled: the choice you make from the Thermostat method option menu changes the selection from the Barostat method option menu.

Relaxation time text box

Enter the relaxation time in ps for the thermostats.

Barostat section

The controls for the barostat method are:

Method option menu

The barostat method is automatically selected based on the input structure, from Martyna-Tobias-Klein for all-atom systems, Langevin for Martini coarse-grained systems, or DPD for DPD systems.

The thermostat method and the barostat method are coupled: the choice you make from the Thermostat method option menu changes the selection from the Barostat method option menu. The exceptions are that you can choose None for the barostat method for any of the thermostat methods, and the Langevin barostat is the only one available with the DPD thermostat method.

Relaxation time text box

Enter the relaxation time in ps in this text box.

Set random number seed option and text box

Select this option to specify a random seed to be used in the simulations. Specifying the seed allows you to reproduce the results, unless other factors affect them. If this option is not selected, a seed is chosen at random.

Energy recording interval text box

Set the recording interval for saving energies, in ps. The resultant number of records to be written is reported to the right.

Reset button

Reset all values for all modes to their defaults.

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