Usage

Q-Force is run in multiple stages. These stages are explained below. At each stage, an options file can be provided to change the default settings with -o file_name. Possible options are listed in Options.

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                 Selim Sami
        University of Groningen - 2020
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usage: qforce [-h] [-o options] file 



  positional arguments:
  ---------------------------------------------------
    file                      Input coordinate file mol.ext (ext: pdb, xyz, gro, ...)     
                              or directory (mol or mol_qforce) name.                      



  optional arguments:
  ---------------------------------------------------
    -h/--help                 show this help message and exit                             
    -o/--options              File name for the optional options.                         


 

1) Creating the initial QM input

et’s assume that we have a coordinate file called mol.ext for a molecule named mol. The extension (ext) can be anything that is supported by ASE (xyz, pdb, gro, …). reate the initial QM input (choosing the QM Software is described in Options) by running the following command qforce mol.ext

This creates a directory called mol_qforce. In it, you can find mol_hessian.inp. Run this calculation on a cluster or locally, and place the output(s) in the same directory.

2) Treating the flexible dihedrals

If your molecule contains flexible dihedrals and if the treatment of flexible dihedrals are not turned off, then fragments and the corresponding QM inputs are created for all unique flexible dihedrals inside the subdirectory fragments with:

qforce mol (or qforce mol_qforce, or qforce mol.ext)

Run these calculations on a cluster or locally, and place the output in the same subdirectory.

3) Creating the force field

Now that all necessary QM results are available, the fitting of the force field is done with:

qforce mol (or qforce mol_qforce, or qforce mol.ext)

4) Output

Done! Q-Force generates several outputs:

• Force field files in GROMACS format (.gro, .itp, .top)
• Force field validation:
  • QM vs MM vibrational frequencies (frequencies.txt, frequencies.pdf)
  • QM vs MM dihedral profile(s) in the fragments subdirectory (.pdf)
• MM vibrational modes (frequencies.nmd) that can be visualized in VMD