Anyone who’s worked with GROMACS knows how essential index groups are when setting up complex molecular dynamics simulations. Whether you’re pulling a specific domain during umbrella sampling or analyzing RMSD for specific atoms, you typically need to create custom index…

Running molecular dynamics (MD) simulations is just one part of the journey. Once a simulation finishes, many researchers face a more frustrating step: importing and analyzing the results. This is especially true when working with multi-step workflows like those used…

When working with molecular systems that involve flexible conformations, dynamics, or simulations, visualizing movements across trajectory frames can quickly become unwieldy. Molecular modelers often need to revisit and align transitions—whether from different simulations, conformational states, or interpolation paths—to better understand…

In molecular modeling, it’s not uncommon to need fine-grained control over how parts of a molecule are optimized. Whether you’re modeling a protein undergoing a point mutation, refining a flexible loop while keeping the rest of the structure in place,…

If you’ve ever tried to work on several molecular modeling tasks at once, you’ll know how frustrating it can be to switch between files, copy molecular structures, or compare results side by side. Whether you’re simulating different conformations, comparing docking…

For many molecular modelers, a common frustration arises when editing a molecular system: what actually happens to the force field setup when you add or delete atoms? Will your simulation break? Will the parameters update accordingly—or will you be left…

If you’ve ever wondered how small changes to your molecule’s structure might affect its biochemical behavior—like modifying a carbon to a nitrogen or tagging on a fluorine—you’re not alone. Medicinal chemists and modelers routinely explore such modifications to improve properties…