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. MD simulation 1-3
    Desmond MD simulation: Prepare a system and run a Desmond MD simulation. Individual frames are then extracted and analyz…
    jcmozzic > Public > Schrodinger workflow examples > Molecular Dynamics > MD simulation > MD simulation 1-3
  2. MD simulation 1
    Desmond MD simulation: Prepare a system and run a Desmond MD simulation. Individual frames are then extracted and analyz…
    jcmozzic > Public > Schrodinger workflow examples > Molecular Dynamics > MD simulation > MD simulation 1
  3. MD simulation 1
    Desmond MD simulation: Prepare a system and run a Desmond MD simulation. Individual frames are then extracted and analyz…
    jcmozzic > Public > Schrodinger workflow examples - old 2019-2 > Molecular Dynamics > MD simulation > MD simulation 1
  4. MD simulation 1-2
    Desmond MD simulation: Prepare a system and run a Desmond MD simulation. Individual frames are then extracted and analyz…
    jcmozzic > Public > TMP > SchrodingerWorkflows2019-4 > Molecular Dynamics > MD simulation > MD simulation 1-2
  5. MD simulation 1-2
    Desmond MD simulation: Prepare a system and run a Desmond MD simulation. Individual frames are then extracted and analyz…
    jcmozzic > Public > Schrodinger workflow examples - old 2019-2 > Molecular Dynamics > MD simulation > MD simulation 1-2
  6. MD simulation 1
    Desmond MD simulation: Prepare a system and run a Desmond MD simulation. Individual frames are then extracted and analyz…
    jcmozzic > Public > TMP > SchrodingerWorkflows2019-4 > Molecular Dynamics > MD simulation > MD simulation 1
  7. MD simulation 1-2
    Desmond MD simulation: Prepare a system and run a Desmond MD simulation. Individual frames are then extracted and analyz…
    jcmozzic > Public > Schrodinger workflow examples > Molecular Dynamics > MD simulation > MD simulation 1-2
  8. MD simulation 1-3
    Desmond MD simulation: Prepare a system and run a Desmond MD simulation. Individual frames are then extracted and analyz…
    jcmozzic > Public > Schrodinger workflow examples - old 2019-2 > Molecular Dynamics > MD simulation > MD simulation 1-3
  9. MD simulation 1-3
    Desmond MD simulation: Prepare a system and run a Desmond MD simulation. Individual frames are then extracted and analyz…
    jcmozzic > Public > TMP > SchrodingerWorkflows2019-4 > Molecular Dynamics > MD simulation > MD simulation 1-3