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Desmond Molecular Dynamics

Schrödinger extension for KNIME Workbench version by Schrödinger

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



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

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.
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.

Input Ports

Model system in CMS or Trajectory format

Output Ports

Trajectory format


Log of multisim
Log of multisim

Best Friends (Incoming)

Best Friends (Outgoing)



To use this node in KNIME, install Schrödinger Extensions for KNIME from the following update site:


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