TransAtlas:

TransAtlas Tutorials

Thanks to the atomistic reconstruction of the more than 8 million intermediate structures found in the TransAtlas conformational transitions, further studies can be conducted with them by means of atomistic Molecular Dynamics simulations. Standard MD simulations, but also biased MD simulations can be performed using the intermediate structures offered by TransAtlas.

TransAtlas tutorials were prepared to ease the gap between the structures ready to be downloaded in the web server, and the following atomistic simulation. Two different tools have been chosen to illustrate the viability and easiness of using TransAtlas intermediate structures in standard and biased MD simulations: MDWeb and Plumed. Three different tutorials are available in TransAtlas tutorials section:

• Atomistic Molecular Dynamics Simulations (using MDWeb): Explains step by step how to use MDWeb server to automatically prepare a TransAtlas atomistic intermediate structure to be used as an input for an atomistic MD simulation.
• Targeted Molecular Dynamics Simulations (using Plumed): Explains step by step how to use Plumed software to run a biased Targeted MD simulation to go from one of the TransAtlas atomistic intermediate structure (origin) to another one (target).
• Path Collective Variables Molecular Dynamics Simulations (using Plumed): Explains step by step how to use Plumed software to run a biased Path Collective Variables MD simulation to go from one of the TransAtlas atomistic intermediate structure (origin) to another one (target) going through the set of intermediate structures computed in a particular conformational transition.