As the author of the tutorial, I want to echo everything @TomPiggot said. The protocol was state of the art about 15 years ago. Now, it is nothing more than perhaps an advanced exercise in working with GROMACS and editing force field files to understand them. Don’t use the protocol for real simulations and certainly don’t use the force field, even if you can find the files. Among other updates, I’m planning a complete rewrite of the membrane protein tutorial. It’s long overdue.
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