DihedralParametrizer GUI

WaNo:

Input files and parameters: (DihedralParametrizer2 tab)

1. Molecule input:

   • Deposit PDB: Import PDB file of the molecule, either from your hard drive or from the Parametrizer WaNo preceding the DihedralParametrizer WaNo in the Workflow.
   • Deposit SPF: Import SPF file containing the nonbonded force field (electrostatic and Lennard Jones) of the molecule, either from your hard drive or from the Parametrizer WaNo preceding the DihedralParametrizer WaNo in the Workflow. Note: Dihedral energy profiles and force-fields are only computed if the spf file contains dihedral information (automatically generated by the Parametrizer).

2. Settings The standard settings are depicted in the screenshot of the DihedralParametrizer WaNo above.

   • Number of Steps: Number of data points for the spline fit of the resulting dihedral force field. Recommended value: 32 or larger. Explanation: To compute the potential of a dihedral angle, each dihedral angle is rotated around 360° in equal sized steps. At each step the dihedral angle is kept fixed at the current value and the rest of the geometry is relaxed using Metropolis Monte-Carlo with a classical force field. DFT single point calculation is then performed on the resulting configuration and the energies of all configurations are used to compute a dihedral force field in form of a spline fit on the data points.
   • Engine: Like QuantumPatch, the DihedralParametrizer employs Quantum Chemistry Engines to compute molecular energies. For the DihedralParametrizer, DFTB (as implemented in DFTB+) and DFT are available. If DFT (requires a Turbomole license and installation not included in the software package) is chosen, additional settings for basis-set and functional are enabled. For reasons of efficiency we recommend to use DFTB, unless your molecule contains atom types not supported in DFTB+ (see list of supported atom types). You can find a description of QM engines here.
   • Advanced settings (we recommed to use standard settings and only use advanced settings, if runs with standard settings do not provide suitable results):
     • scf iterations: The number of iterations of the above mentioned algorithm. In each iteration, the dihedral force-field of the previous step is applied for the relaxation of the molecule, leading to an increased accuracy of the force-field energy. At least 2 scf iterations should be used.
     • MC step multiplier: For each evaluation point of the dihedral potential, the remaining molecular configuration is relaxed to avoid clashes. For a very complex molecule, the standard number of MC relaxation steps can be scaled up using this value.
     • evaluation points: Number of random dihedral configurations used to assses quality of the dihedral forcefield (see CorrelationPlots.png in output files) validated against single point DFT/DFTB values.

Parallelization and Performance: (Resources tab)

DihedralParametrizer is parallelized and scales almost linarly with the number of processors up to the total number of performed QC computations. This number increases with the number of dihedral angles in the molecule and "Number of steps" (see above). For a molecule with only a single dihedral angle, e.g. the number of cores should be "Number of steps" plus one or lower. The required memory depends on the size of your compound. For average sized small organic compounds (~100 Atoms) 1000MB are sufficient. Check the manual of your DFT engine for details.

For every option not checked in the „Resources“ tab, the server defaults that depend on your HPC machine will be used. Check individual options to modify specific values.

Recommended resources for DihedralParametrizer:

Resource	Recommendation
CPUs per Node:	The calculation of each data point (see „Number of Steps“ above) can be performed on a CPU each. E.g. for 32 data points, set CPUs per Node to 32 and accordingly. If the number of datapoints is larger than the number of CPUs available per node, use number CPUs available.
Number of Nodes:	1 (No parallelization on more than a single node available)
Memory:	1000MB, see above under „Hardware Parameters“.
Walltime:	Depending on the size of the compounds and the number of data points and the number of dihedrals of your molecule, the parametrization takes between 1h and 24h.
Queue:	Default

Output Files

Filename	File description	Interface to module...
molecule.pdb	PDB-file containing atom positions.	Deposit
dihedral_forcefield.spf	Force-field file for Deposit including the nonbonded force field (partial charges and Lennard-Jones parameters) and the dihedral force field computed for this module.	Deposit
iter_X/snap_files_LJ/*.png	Plots of dihedral forcefield (dihedral_.png), VdW contribution to the forcefield (vdw_only_.png) and DFT(B) contribution to the forcefield (dft_only_*.png).	None