Parametrizer GUI

WaNo and Overview
Parametrizer WaNo

Input files and parameters

Molecule Settings:

  • Molecule (Mol2): Input of a 3D molecular structure in the mol2-file format.
  • Molecule Identifyer: three-digit alphanumeric string that is used to label the molecule throughout the workflow in various output files.
  • Optimize Molecule: Check this box to perform geometry optimization of your compound.
  • Charge: Chose the charge state of the molecule, which shall be parametrized.
  • Multiplicity: Select the multiplicity of the molecule which relys on the number of unpaired electrons. Therefore, select 1 for a system, having just paired electons (singlet), select 2 for a radical system, having one unpaired electron (doublet), or select 3 (triplet) for a system, having two unpaired electrons.
  • Excited State of Interest: Usually, the molecular parameters for the groundstate S0 and requested and therefore select 0 in this dropdown. However, this tool also offers you to optimize the molecule e.g. in the S1 state, selecting 1. To ensure a stable optimization we request the following: select SCF Convergence tight or extreme same for Geometry Convergence, or perform first a optimization in the groundstate and another in the excited state.

DFT Engine:

  • Engine: Chose the DFT Engine for geometry optimization and computation of partial charges. Currently available: Turbomole (DFT, user needs to have a Turbomole license), Psi4 (DFT) and DFTB+ (DFTB). For details, check the DFTEngines-section
  • Engine-specific settings:
    • Turbomole:
      • Partial Charge Method: Electrostatic potential fit (EPS), Mulliken available or No charges (just required when you want to calculate excitation energies Meta-hybrid GGA e.g. M06-2X functional)
      • D3 Dispersion Correction: Account for Pauli-repulsion. We recommend to use this option for geometry optimization.
      • static_polarizability: This is required for specific QuantumPatch runs. It will print out the static polarization tensor of the molecule.
      • Functional and basis set: Check the Turbomole manual for details. We recommend to use B3LYP, SVP and the ESP-fit method for computation of partial charges.
      • Preoptimization: Preoptimization of the molecular geometry with XTB or DFTB may achieve a significant reduction of computation time. We recommend to use DFTB for molecules containing only elements supported by DFTB (see list of supported atom types ) or XTB if the molecule contains additional elements.
      • SCF and Geometry convergence sets the Turbomole convergence criterion. For the subsequent computation of sensitive quantities such as excitation energies in QuantumPatch, we recommend to use the Tight or Extreme option, but stick to Normal otherwise.
      • Analysis options: enables optional tasks after the Turbomole calculation. Currently, Estimate electrostatic disorder and Generate orbital plots are available.
    • Psi4:
      • Partial Charge Method: Electrostatic potential fit (EPS) or Mulliken available. ESP recommended.
      • D3 Dispersion Correction: Account for Pauli-repulsion. We recommend to use this option for geometry optimization.
      • Functional and basis set: Check the Psi4 manual for details.
      • Preoptimization: Preoptimization of the molecular geometry with XTB or DFTB may achieve a significant reduction of computation time. We recommend to use DFTB for molecules containing only elements supported by DFTB (see list of supported atom types ) or XTB if the molecule contains additional elements.
    • DFTB+:
      • Partial Charge Method: Improved Charge Model 3 (CM3) or Mulliken available. CM3 recommended.
      • D3 Dispersion Correction: Account for Pauli-repulsion. We recommend to use this option for geometry optimization.
    • XTB:
      • Partial Charge Method: Charge Model (CM5) or Mulliken charges are available. CM5 is recommended for GFN XTB version 1 and Mulliken for GFN XTB 2 (GFN2 does not support CM5 right now, therefore, just Mulliken charges can and will be calculated, even if CM5 is selected).
      • SCF convergence sets the XTB convergence criterion. Normal is recommended.
      • Optimization cycles sets the number of runns which are used to get an optimized structure. 2000 should be enough to obtain a final structure.
      • GFN selects the version of XTB. GFN 2 is recommanded.

Output Files - Inputs for further modules

Molecular structure and forcefield files

Filename File description Interface to module...
molecule.pdb pdb-file containing atom positions and bond information of the (optimized) molecular structure. Deposit or DihedralParametrizer
molecule.spf Force-field file for Deposit including partial charges and Lennard-Jones parameters as well as a list of dihedral angles for the DihedralParametrizer. Deposit or DihedralParametrizer
output_molecule.mol2 mol2-file for general use. Can be read into subsequent Parametrizer runs to run additional analysis e.g. with other functionals as used in the inital optimization. e.g. Parametrizer

Single molecule analysis output

Electronic structure information

Information on electronic structure is printed to the file mol_data.yml. The detailed output depends on the selected settings, chosen analysis mode (Estimate electrostatic disorder or Generate orbital plots) and is exemplified for both options below:

  • mol_data.yml file contains always the ID of the HOMO and LUMO and their energies, the dipole moment as xyz-vector and the total energy of the molecule.
  • the first five excitation energies (1. - 5.) and their lifetimes are listed, when the option:Excited State of Interest=1 is selected.
  • the analysis of several constructed ESP surfaces are listed and the electrostatic disorder is estimated, as illustrated below, when analysis options:Estimate electrostatic disorder is selected.
mol_data.yml content of calculation with selected options:Estimate electrostatic disorder mol_data.yml content of a calculation with selected excitation energy 1

Plotting molecular orbitals

The Parametrizer can also be used to visualize the HOMO and LUMO of the molecule if the Analysis option:Generate orbital plots is selected. Thus, the folder DFT_runtime_files contains another folder vmd_output with the following files: .tcl, .plt, .sh and .xyz. If VMD is installed, you can directly creat a png-file using: \ bash plot_homo.sh for the HOMO and bash plot_lumo.sh* for the LUMO. Furthermore, the command vmd -e plot_homo.tcl opens VMD and creates a representation of the molecule and orbital.

Example:Orbital plots for anthracene

Raw DFT runtime data

This folder contains all the files, which were created during the calculation. For example, if Turbomole is selected as a DFT engine, a TM.out will be included, summarizing the individual calculation steps and their results. Thus, this folder can be used to track down the potential source of crashed simulations.

Parallelization and Performance

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 Parametrizer:

Resource Recommendation
CPUs per Node: The Parametrizer is parallelized up to a single node. We recommend to use a full node especially for larger compounds, if Turbomole or Psi4 is used.
Number of Nodes: 1
Memory: 1500MB
Walltime: Computation time depends strongly on DFTEngine, size of the compound and number of cores, whether or not the geometry is optimized and if so, also on the quality of the initial geometry provided as input.
Queue: Default

Trouble shooting

  • Calculations of excited states, using M06-2X, require to choose the following options:

    • Partial Charge Method: No Charges
      Thus, partial charges for excited molecules, using M06-2X, cannot be calculated, but excitation energies.

 

 

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