A set of example systems that can be used for SEEKR2 calculations, as well as additional tests for SEEKR2 validation.
The input files can be found at:
systems/
trp_cage_files/
input_trp_cage.xml
superoxide_dismutase_files/
input_sod.xml
trypsin_benzamidine_files/
input_tryp_ben_elber.xml
input_tryp_ben_multidim.xml
input_tryp_ben_mmvt_namd.xml
input_tryp_ben_mmvt.xml
input_tryp_ben_mmvt_hmr.xml
toy_systems/
input_entropy_barrier_elber.xml
input_entropy_barrier_multidimensional.xml
input_entropy_barrier.xml
input_muller_potential_cvs.xml
input_muller_potential_multi.xml
input_muller_potential.xml
input_simple_quadratic_potential.xml
Any one of these input files may be used as input to a SEEKR2 calculation.
Example:
python ~/seekr2/seekr2/prepare.py systems/trypsin_benzamidine_files/input_tryp_ben_mmvt.xml
Additionally, these input files are intended to be useful as references for crafting SEEKR2 input files for your own systems of interest.
This repository also contains a number of tests that further validate SEEKR2 on the systems in this repository. They can be run with the following command:
cd tests
pytest
To test all input scripts (for validation purposes), run the following script:
python tests/run_me_test_systems.py