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When using ARAP (As-Rigid-As-Possible) Interpolation to generate protein conformational transitions, an essential but sometimes overlooked step is how the structural connectivity—also known as ARAP edges—is defined. For molecular modelers preparing simulations or building transition pathways, getting the connectivity right can…

Free energy calculations of ligand binding or unbinding can be extremely powerful—but preparing input files often feels more painful than productive. One recurring challenge is extracting the atomic coordinates of molecules along a computed reaction path. If you’ve ever run…

Creating molecular animations isn’t just about visualizing structures—it’s about communicating insights clearly. When zooming into molecular systems, many researchers use the Zoom camera effect in SAMSON. But there’s a subtle limitation: it only moves the camera along its view direction,…

Molecular modelers often face a recurring challenge when studying conformational changes in large biomolecular systems: how to generate a realistic trajectory between two known structural states. This issue becomes more complicated when the two states differ significantly, as is the…

Setting up GROMACS for molecular dynamics simulations can be a real roadblock for many researchers. Between compiling the package, ensuring all dependencies are correctly met, and navigating version compatibility issues, it’s no surprise that time is often spent troubleshooting before…

Molecular dynamics simulations are rarely one-size-fits-all. If you’ve ever needed to tweak temperature coupling, adjust time steps, or fine-tune constraints for your system, you’re not alone. Default settings are great for getting started, but real science often calls for customization.…

One of the more time-consuming challenges in molecular modeling is having to constantly switch between different tools or manually write scripts to bridge gaps between specific needs and the capabilities of existing software. Whether you’re trying to customize a simulation…

When preparing a molecular dynamics simulation involving pulling—such as center-of-mass (COM) pulling—one of the most overlooked yet critical steps is correctly defining the simulation box size. A common pitfall for modelers is encountering artifacts due to improper box dimensions, especially…

One of the most common questions molecular modelers have when setting up docking experiments is: “Where should I define the search space?” Whether you’re targeting a known binding pocket or screening broadly across the protein, defining the search domain correctly…