Author: OneAngstrom

When preparing scientific animations to explain molecular mechanisms or communicate results, clarity is key. A frequent challenge modelers face is: how do you selectively reveal elements of your molecular system at just the right time during an animation? Whether it’s…

When you’re deep in molecular modeling, every click counts. Whether you’re generating a nanotube, applying a rigid-body transformation, or fine-tuning a molecular structure, switching between modeling tasks often means changing your toolset. And in SAMSON, editors are those tools. Editors…

One common challenge in molecular modeling is identifying the motions that allow biomolecules, such as proteins, to adopt conformations that open or close binding pockets. This task is particularly relevant when working on ligand docking, drug design, or analyzing functional…

Designing accurate nanoscale structures is a challenge many molecular modelers face, especially when trying to create periodic or symmetric systems like carbon nanotubes. Manually duplicating and arranging atoms to form a 3D tube with precise geometry can be both time-consuming…

Customizing molecular dynamics (MD) parameters in GROMACS can often feel intimidating, especially for those used to working outside the command line. Researchers might want to experiment with different time steps, thermostats, or barostats, but worry about editing raw .mdp files.…

When preparing membrane protein systems for simulation, one of the most repetitive and time-consuming tasks is building a lipid bilayer around your protein. From aligning the protein to carefully setting up two asymmetric lipid layers, molecular modelers often rely on…

One common challenge in the analysis of molecular simulation results is making sense of how ligands move in and out of protein binding pockets. While numerical data can help quantify these processes, the ability to intuitively visualize the motion of…

When working with molecular models, making consistent changes across multiple atoms, bonds, or residues can be tedious and error-prone. Whether you’re adjusting atom positions, reassigning element types, or updating other attributes, repeating the same modification individually is inefficient. If you’ve…

In molecular modeling, building a lipid bilayer around a membrane protein is often a necessary step for meaningful simulations. Whether you’re preparing a system for molecular dynamics or just visually analyzing structural interplay, constructing a realistic lipid environment can be…

In molecular dynamics setups using GROMACS, defining appropriate index groups is essential when applying center-of-mass (COM) pulling between specific parts of a molecular system. However, this can be a challenge, especially when your regions of interest aren’t part of GROMACS’…