seekr2_systems

A set of example systems that can be used for SEEKR2 calculations, as well as additional tests for SEEKR2 validation.

Overview of systems

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.

Tests

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