BioExcel
Popular repositories
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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_amber_md_setup 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.
- biobb_wf_md_setup Public
This tutorial aims to illustrate the process of setting up a simulation system containing a protein, step by step, using the BioExcel Building Blocks library (biobb).
- 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_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_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_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_flexserv Public
This tutorial aims to illustrate the process of generating protein conformational ensembles from 3D structures and analysing its molecular flexibility, step by step, using the BioExcel Building Blocks library (biobb).
- biobb_wf_flexdyn Public
This tutorial aims to illustrate the process of generating protein conformational ensembles from 3D structures and analysing its molecular flexibility, step by step, using the BioExcel Building Blocks library (biobb).
- 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).
