- Automatically generate Gromacs structure files from Gaussian output files.
- Place gaussian outputs in the data/gaussian_outputs file
- Requires python environment with acpype. pip install -r requirements.txt to get modules
What it does Antechamber - convert .log to mol2 antechamber and tleap. parameterises molecules Acpype - creates topologies and gromacs files from antechamber outputs Creates new itp and topologies if needed (for mixtures) Stacks gromacs structures to create a box (mixture) insert second molecule type generates the necessary files (job script) to run an energy minimisation
COMMANDS
- auto-box (MOLECULE_NAME) (TOTAL NUMBER OF MOLECULES IN SIMULATION BOX) Construct a gromacs simulation box of a single molecule
- mix-gen (MOLECULEA_NAME) (MOLECULEB_NAME) (PERCENTAGE OF MOLECULEA) (PERCENTAGE OF MOLECULEB) (TOTAL NUMBER OF MOLECULES IN SIMULATION BOX) Construct a simulation box of a mixture fo molecules. Note molecule A should be the component with the largest number of molecules