SIMONAPreprocessor
POEM++ Moves
D_POEM_Moves.png
Moves (A)
  • Dihedral rotations: Allows rotations of the protein dihedrals. You have to enter the change per step in the box beside.
    • Manual: If this option is checked only the angles you selected will be changed. For a description how to select angles click here.
    • Mainchain dihedrals: If this option is checked only the angles of the mainchain will be changed.
    • Sidechain dihedrals: If this option is checked only the angles of the sidechains will be changed.
  • Rigid body translations: Enables your entire molecule to move. You have to enter the change per step in the box beside.
  • Rigid body rotations: Enables your entire molecule to rotate. You have to enter the change per step in the box beside.
Expert settings (B)
  • Angle bends: Changes the angle between the bond of atoms (i, j) and the bond between the atoms (j, k). You can specify which angles are allowed to change in the box beside. For syntax explanation click here. In the other box put the change per step.
  • Bond stretching: Changes the distance $ d_{ij} $ between the Atoms i and j. You can specify which bonds are allowed to change in the box beside. For syntax explanation click here. In the other box put the change per step.
  • Ramachandran biased moves: Prefers the Ramachandran energies in the Ramachandran regions aproximated by circles.
  • Ramachandran biased moves (Madrid version): Allows only energies within the Ramachandran regions defined by Abhinav, Verma.
  • Conditional streered MC simulations: This option allows you to manipulate the molecules while simulating.
  • Forced steered MC simulations: This option allows you to manipulate the molecules while simulating.
  • Local moves: Allows local dihedrals to move without changind the rest of the chain. Put the change per step in the box beside.
  • Add peptide spec: Needed for Local moves.


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