DihedralParametrizer Documentation

Customized Dihedral Force-Fields

To enable efficient simulation of conformational changes of molecules during the deposition process, rotations around single bonds are applied in Deposit - so called dihedral moves. The change in energy connected to such a dihedral move is computed using dihedral force-fields. These force-fields then determine the flexibility of the molecules during deposition. As the molecular packing and therefore the electronic structure in thin films are highly sensitive to the flexibility of the deposited molecules, an accurate, molecule-specific description of the energy profile of the dihedral rotations is essential.

The DihedralParametrizer therefore automatically computes dihedral force-fields for organic compounds using quantum-chemistry. The principle works as follows:

For each dihedral angle:

  1. Rotate the the side group step-wise around the single-bond
  2. For each step:
    • Keep the angle fixed and relax the rest of the molecule, to avoid clashes
    • Compute the energy for this configuration using one of our DFTEngines
    • Correct the energy by internal force-field values later applied in Deposit

For molecules with multiple dihedral angles, this protocoll is modified to account for correlation effects in conformational changes.

The resulting 360° energy profiles are then tabulated for efficient evaluation during the deposition process. As an example, you can find the energy profiles for one of the dihedral angles of alpha-NPD at the bottom of this page.

Product specifications

  • Input:
    • Optimized molecular geometry (pdb file, from Parametrizer)
    • Force-field file containing non-bonded parameters and information on flexible dihedral angles (spf file, from Parametrizer)
  • Output:
    • Complete force-field files for Deposit containing Lennard-Jones parameters, partial charges and customized dihedral force-fields.
    • Plots of dihedral energy profiles
  • Requirements
    • IntelMPI 18.3 or larger

Example: alpha-NPD

alpha-NPD alpha-NPD dihedral profile

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