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MD simulation 1

Desmond simulation

Prepare a system and run a Desmond MD simulation. Individual frames are then extracted and analyzed in terms of hydrogen bond network and atom distance.

[Requires: Desmond] [Keywords: Moleclar dynamics simulation, trajectory, snapshots, jobcontrol, distance, hydrogen bond, atom selection]

Neither the system definition nor the trajectory is saved with the workflow as it can be very large. If you don't want torerun the workflow from the beginning you can still reset and rerun the analysis section (starting from the Alignbinding sites node).This workflow can be run only on Linux. Desmond simulation:Prepare a system and run a Desmond MD simulation. Individual frames are then extracted and analyzed in terms of hydrogen bond network and atom distance.[Requires: Desmond] [Keywords: Moleclar dynamics simulation, trajectory, snapshots, jobcontrol, distance, hydrogen bond, atom selection] Very shortsimulation~ 30 min on 4 CPUsCreate an archive with the trajectory filesInspect the systemCenter the proteinat the origin List the running jobsInformationon running jobsGet PDB Protein PreparationWizard Desmond SystemBuilder Desmond MolecularDynamics Desmond TrajectoryManipulation Run Maestro ChemistryExternal Tool Table Viewer Job Control Job Control Neither the system definition nor the trajectory is saved with the workflow as it can be very large. If you don't want torerun the workflow from the beginning you can still reset and rerun the analysis section (starting from the Alignbinding sites node).This workflow can be run only on Linux. Desmond simulation:Prepare a system and run a Desmond MD simulation. Individual frames are then extracted and analyzed in terms of hydrogen bond network and atom distance.[Requires: Desmond] [Keywords: Moleclar dynamics simulation, trajectory, snapshots, jobcontrol, distance, hydrogen bond, atom selection] Very shortsimulation~ 30 min on 4 CPUsCreate an archive with the trajectory filesInspect the systemCenter the proteinat the origin List the running jobsInformationon running jobsGet PDB Protein PreparationWizard Desmond SystemBuilder Desmond MolecularDynamics Desmond TrajectoryManipulation Run Maestro ChemistryExternal Tool Table Viewer Job Control Job Control

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To use this workflow in KNIME, download it from the below URL and open it in KNIME:

Download Workflow
On NodePit since: 2020-08-12
Last update: 2026-01-17
Created with KNIME version: v4.1.0
Tags: Molecular DynamicsDesmondTrajectorySnapshotsJobcontrolDistanceHydrogen BondAtom Selection

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