Tools
Parametrization Tools
You may find some parametrization tools in the following public repositories:
-
Automated selection and grouping of internal coordinates. https://github.com/dpadula85/SelIntCoords
-
Automated generation of initial topologies. https://github.com/jpablogalvez/gen_FF
-
Generation of fcc files from the output of different QM codes. https://github.com/jcerezochem/fcc_tools
Conversion Tools
LAMMPS conversion
You may find the conversion tool as well as some examples in the compressed file below.
CHARMM conversion
You may find the conversion tool as well as some examples in the compressed file below.
Validation Tools
We have developed a set of tools to assist during the force field validation.
You may find the validation tools as well as one test case in the following repository:
- JoyceTools: a package to facilitate the use of JOYCE Force Fields. https://gitlab.com/jcerezochem/joycetools
The proposed validation protocol consists of 4 steps each drawing comparisons between the MM and QM descriptions ranging from the static to the dynamical picture:
i) Ground/minimal energy states.
ii) Normal modes under the local harmonic approximation.
iii) Relaxed energy scans across the flexible degrees of freedom.
iv) Energy fluctuations for snapshots drawn from a MD run.
The validation tools specifically automatize the first and third validation test. The second test is readily available as part of the JOYCE output and has a dedicated keyword. The fourth test does not have a fixed routine, since it depends on the specific DFT software at the users disposal. For more details, please check the validation steps on any of the JOYCE Tutorials.