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GROMACS tutorial. a. GROMACS is the program we use to run molecular dynamics simulations. It is essential when doing this tutorial that you understand WHAT the command is doing, not just type it in to the next step. ... Do the lysozyme in water tutorial, write down what every command does after looking it up in the GROMACS user manual. Could. Right-click on the current selection in the Document view or in the Viewport and in the context menu go to Expand selection > Advanced. 3. In the pop-up dialog, set Water as the Node type, and choose beyond some distance that is outside of the active site. You can click on the auto-update option to see the selection. Click OK to select.

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