Desmond Molecular Dynamics

Molecular dynamics jobs simulate the Newtonian dynamics of the model system, producing a trajectory of the particles, coordinates, velocities, and energies, on which statistical analysis 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 analysis. 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.

Backend implementation

Options

Column containing input

Select the column containing input structure

Output Column Structure

Choose the output columns:

Input plus Output - The input columns are included in the output.

Output replaced within Input columns - The output columns are the same as the input, with the output structures replacing the input column selected

Output only - Only Output structures

Settings...

On clicking "Settings" button, this node brings up the "Molecular Dynamics" Python panel for configuration.

Parameter flow variables

Any valid option for this node can be specified through flow variables. Only String variables are accepted.
Usage:
Flow variable prefix keyword: DesmondMD
Note: To specify an option as flow variable, the flow variable name should be like:
keyword-option_name for single-dash option
keyword--option_name for double-dash option

To add a new option with value, specify the option_name and the corresponding value through flow variable.

To add a new option without value, specify the option_name and the value as _on_ through flow variable.

To override an existing option's value in the command line, just specify the option_name and the new value through the flow variable.

To remove an existing option without a value, specify the option_name and the value as _off_ through the flow variable.

To remove an existing option with a value, specify the option_name and the value as _rm_ through the flow variable.

Views

Log of multisim

Log of multisim

Workflows

• MD simulation 1KNIME Hub
• MD simulation 1KNIME Hub
• MD simulation 1-2KNIME Hub
• MD simulation 1-2KNIME Hub
• MD simulation 1-3KNIME Hub
• Show all 6 workflows

Links

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Developers