Protein docking can produce a long list of plausible-looking poses. When the binding site is already known—or at least suspected—searching every possible orientation may spend time on regions that are unlikely to matter. The challenge is to narrow the search…

A molecular model can be ready to share long before it is ready for everyone to edit. Maybe you want a colleague to inspect a structure, a research group to reuse a document, or a collaborator to access a resource…

Building a polymer from molecular fragments can become tedious quickly. You may need to connect several different monomers, repeat sections, control selected bond types, and keep track of which fragment connects to which. Typing a long chain by hand makes…

Finding a DNA origami structure is only the first step. Molecular modelers often need to answer a more practical set of questions: Can this design be opened in my software? Can I inspect or adapt it? What should I save,…

A Potential of Mean Force (PMF) can turn umbrella-sampling results into a profile that is easier to interpret. But a smooth-looking curve is not the whole story: if parts of the reaction coordinate are poorly sampled, the result deserves closer…

Preparing a molecular dynamics workflow repeatedly can be tedious—and it is easy to introduce small inconsistencies when each project is configured by hand. GROMACS Wizard batch computations address this problem by letting you apply the same workflow to many starting…

Installing molecular modeling software is only half the job. The other half is figuring out what to do when the application opens: Where is it installed? How do you launch it again? Is it still downloading components, or do you…