Garleek is composed of two small programs:
garleek-prepare, used to patch the QM-provided input file with correct atom types
garleek-backend, which interfaces the QM program with the MM engine to make them understand each other
garleek-prepare will inject the necessary
garleek-backend calls in the QM input file, so you should only run the following command. Everything else is handled automatically.
garleek-prepare --qm gaussian --mm tinker --ff mm3 --types uff_to_mm3 INPUTFILE
INPUTFILE: QM input file to be patched and renamed. For example,
file.inwould be renamed as
file.garleek.in. Currently supported: Gaussian input files (
--qm: QM program handling the QM/MM calculation. Currently supported keywords include: gaussian, gaussian_09a, gaussian_09b, gaussian_09c, gaussian_09d, gaussian_16.
--mm: MM engine to be used. Currently supported keywords include: tinker, tinker_qmcharges. Read below for more details.
--ff: force field to be used in the MM calculation. Supported files and keywords depend on the value of
--types: dictionary handling the conversion between the MM atom types provided in the original input file and those the MM engine actually needs for the chosen force field. Supported files and keywords depend on the value of
qm. Usually is a simple two-column plain-text file that contains
Original-MM-type Converted-MM-typemappings. This file is used to replace the original types in
MyInputFile.in. Matching is case-insensitive, but the file must list them ALWAYS uppercased.
TIP: Updated CLI arguments will be always available if you run
For more details and specific use-cases, please refer to the tutorials section. Begin with the first one by clicking here: A simple CH4 molecule.