FastFold for Calvados molecular dynamics simulations


I just found a platform that lets you run Calvados force field simulations without touching a terminal.

It's called FastFold, and it has a built in app for Calvados molecular dynamics simulations.

Here's how simple it is:

Go to FastFold, click on Apps, and open Calvados.

You can input your own sequence of interest, or start with the examples section.

There are several proteins to choose from, and I would recommend starting with lysozyme.

Click on it and you'll be prompted to a settings page for the simulation

You can leave everything on default or adjust the parameters yourself. Click Run simulation

In a matter of minutes, you'll get a full set of metrics from your simulation.

Free energy landscape, Rg, RMSD, and more, all plotted and ready to explore.

I also noticed something that got my attention. The plots on this platform are generated using MD Quick Plot, a tool I built myself. Seeing other platforms adopt tools I develop is one of the best kinds of validation.

From there, click Open in and select Py3Dmol.

This takes you to a page where you can see your MD simulations run in 3D.

That's the whole process!!

If you try it out, let me know how it goes in the comments. I would love to hear your experience!!

Link to FastFold: https://lnkd.in/gTTH-Si9

Best,

Omar

© ProteinReach|2026 SciLearningWorkshops LLC


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