4. rigidmol: Rigid Molecular Clusters Using Force Fields

rigidmol (which was called rigidmol-optimizer in old versions of ABCluster) supports the global optimization of molecular clusters described by CHARMM force field. The molecules in rigidmol are assumed to be rigid, meaning that the internal degrees of freedoms (bond lengths, bond angles, dihedral angles) are kept frozen during the optimization. For small molecules, this is a very good approximation.

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Contents:

• 4.1. CHARMM Force Field
• 4.2. Example: (H2O)6
• 4.3. Example: Build Parameter File for (NHCH3)2CO
  • 4.3.1. New Way: Automatically Building
  • 4.3.2. Old (and out-of-date) Way: Manually Building
• 4.4. Example: Pincer and Water Using topgen and Multiwfn
  • 4.4.1. Calculate Parameters
  • 4.4.2. Global Optimization
• 4.5. Example: Li+, Na+, and Cs+ in (C6H6)6
• 4.6. Example: HNO3(H2O)10 in Electric Field