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_structure_checking Public
This tutorial aims to illustrate the process of checking a molecular structure before using it as an input for a Molecular Dynamics simulation using the BioExcel Building Blocks library (biobb).
- biobb_wf_protein-complex_md_setup Public
This tutorial aims to illustrate the process of setting up a simulation system containing a protein in complex with a ligand, step by step, using the BioExcel Building Blocks library (biobb).
- 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).
- biobb_wf_mem Public
This tutorial aims to illustrate the process of analyzing a membrane molecular dynamics (MD) simulation using the BioExcel Building Blocks library (biobb).
- biobb_wf_godmd Public
This tutorial aims to illustrate the process of computing a conformational transition between two known structural conformations of a protein, step by step, using the BioExcel Building Blocks library (biobb).
- 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).
- biobb_flexserv Public
Biobb_flexserv is a BioBB category for biomolecular flexibility studies on protein 3D structures.
- 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).
- biobb_wf_autoencoder Public
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