BioExcel
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gromacs-2022-cp2k-tutorial
gromacs-2022-cp2k-tutorial PublicSample inputs and tutorial for GROMACS-2022/CP2K QMMM interface
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cp2K_qmmm_tutorials_for_biological_simulations
cp2K_qmmm_tutorials_for_biological_simulations PublicSeveral QM/MM tutorials for biological simulations adapted to CP2K. Tutorials adapted from AMBER, GMX, NAMD and CPMD softwares.
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Repositories
- biobb_wf_dna_helparms Public
This tutorial aims to illustrate the process of extracting structural and dynamical properties from a DNA MD trajectory helical parameters, step by step, using the BioExcel Building Blocks library (biobb).
bioexcel/biobb_wf_dna_helparms’s past year of commit activity - biobb_wf_amber Public
This tutorials aim to illustrate the process of setting up a simulation system containing a protein, step by step, using the BioExcel Building Blocks library (biobb) wrapping the Ambertools MD package.
bioexcel/biobb_wf_amber’s past year of commit activity - biobb_wf_cmip Public
This tutorial aims to illustrate the process of computing classical molecular interaction potentials from protein structures, step by step, using the BioExcel Building Blocks library (biobb).
bioexcel/biobb_wf_cmip’s past year of commit activity - biobb_wf_pmx_tutorial Public
This tutorial aims to illustrate how to compute a fast-growth mutation free energy calculation, step by step, using the BioExcel Building Blocks library (biobb).
bioexcel/biobb_wf_pmx_tutorial’s past year of commit activity - biobb_structure_utils Public
Biobb_structure_utils is the Biobb module collection to modify or extract information from a PDB structure file, such as pulling out a particular model or chain, removing water molecules or ligands, or renumbering or sorting atoms or residues.
bioexcel/biobb_structure_utils’s past year of commit activity - biobb_pytorch Public
Biobb_pytorch is the Biobb module collection to create and train ML & DL models using the popular PyTorch Python library.
bioexcel/biobb_pytorch’s past year of commit activity - biobb_pmx Public
Biobb_pmx is the Biobb module collection to perform PMX (http://pmx.mpibpc.mpg.de) executions.
bioexcel/biobb_pmx’s past year of commit activity - biobb_pdb_tools Public
bioexcel/biobb_pdb_tools’s past year of commit activity - biobb_model Public
Biobb_model is the Biobb module collection to check and model 3d structures, create mutations or reconstruct missing atoms.
bioexcel/biobb_model’s past year of commit activity
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