NodeDesmond System Builder

Source

The System Builder panel allows you to set up a biological system consisting of proteins, ligands, explicit solvent, membrane, and counter ions, so that you can perform simulations on the system with Desmond.

Backend implementation

$SCHRODINGER/utilities/multisim
Input ports
  1. Structure in Maestro format Type: Data
    Input structure in Maestro format
Output ports
  1. CMS files Type: Data
    CMS file
  1. Desmond simulation
    Molecular Dynamcis Desmond Trajectory Snapshots Jobcontrol Distance Hydrogen Bond Atom Selection
    Prepare a system and run a Desmond MD simulation. Individual frames are then extracted and analyzed in terms of hydroge…
    schroedinger > Public > Schrodinger_workflow_examples > Molecular Dynamics > MD simulation > MD simulation 1-3
  2. Desmond simulation
    Molecular Dynamics Desmond Trajectory Snapshots Jobcontrol Distance Hydrogen Bond Atom Selection
    Prepare a system and run a Desmond MD simulation. Individual frames are then extracted and analyzed in terms of hydroge…
    schroedinger > Public > Schrodinger_workflow_examples > Molecular Dynamics > MD simulation > MD simulation 1-2
  3. Desmond simulation
    Molecular Dynamics Desmond Trajectory Snapshots Jobcontrol Distance Hydrogen Bond Atom Selection
    Prepare a system and run a Desmond MD simulation. Individual frames are then extracted and analyzed in terms of hydroge…
    schroedinger > Public > Schrodinger_workflow_examples > Molecular Dynamics > MD simulation > MD simulation 1