Schrödinger KNIME Extensions allow scientists to protoype, validate, automate, and deploy multi-step workflows. Schrödinger’s KNIME Extensions Associate Product Manager Jean-Christophe Mozziconacci is dedicated to developing valuable KNIME workflows for our users and providing guidance for efficient execution of these workflows.
Q. How can I set up and run an MD simulation using KNIME?
A. You can use the Desmond System Builder node to set up your system, and the Desmond Molecular Dynamics node to perform the calculation. You can easily run the same protocol on several structures (e.g., protein-ligand complexes) by supplying several input table entries. To track the calculation’s progress, add the Chemistry external tool node and configure it to use the jobcontrol browser display (-g) option. For a straightforward example workflow using all of these elements, see the Desmond simulation 1 workflow example.
Once the job completes, you can use the Desmond Trajectory Extract Frames node to obtain snapshots from the trajectory for a part of the structure for inspection and/or analysis. For an example of this, see the Desmond simulation 1-2 workflow example where the solvent and counter ions are excluded from extraction using the ASL expression: not (mol.atoms 3) AND not (mol.atoms 1).
These extracted snapshots can be used as input for other workflows, and event analysis data can be mined with Cheminformatics nodes (see the Desmond simulation 1-2 and 1-3 workflow examples). Setting up a KNIME workflow for post-processing your MD simulation can save a lot of time in the long run, because you can design analyses specific to your system of interest (e.g., to count the number of hydrogen bonds in the system for each snapshot, to count the number of hydrogen bonds to the ligand only; see Desmond simulation 1-2 workflow example), and run the various structures through your KNIME workflow without having to repeatedly configure the Desmond Simulation analysis tools in Maestro for each structure.
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Q. In the last newsletter, you talked about KNIME workflows that can be run directly from the Maestro interface. Do you have any examples I can use to get started with?
A. There are several example workflows already embedded in your Schrödinger 2012 installation. You can install the ones you are interested in by navigating within Maestro to Workflows > KNIME Workflows > Install Examples.
You can explore and download additional workflows from the KNIME Workflows for Maestro page.
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