GROMACS Plugin for AiiDA

aiida-gromacs on PyPI

Tutorial with pre-loaded user environments for using aiida-gromacs to produce provenance workflows for biomolecular simulations. This Jupyter Notebook (.ipynb) tutorial follows the first six steps of Justin Lemkul's lysozyme tutorial (http://www.mdtutorials.com/gmx/lysozyme/). This example will guide a new user through the process of setting up a simulation system containing a protein (lysozyme) in a box of water, with ions. Each step will contain an explanation of input and output, using typical settings for general use.

Tutorial with pre-loaded user environments for using aiida-gromacs to produce provenance workflows for biomolecular simulations. This Jupyter Notebook (.ipynb) tutorial follows the steps to embed a receptor protein in a lipid membrane. This example will guide an experienced user through the process of downloading, tidying up, orientating, coarse-graining, embedding, and solvating a receptor protein, ready for simulation. Each step will be wrapped in aiida-gromacs commands to capture its inputs and outputs.