Author: OneAngstrom

Working with multiple replicas of a protein system is common practice when setting up coarse-grained (CG) molecular dynamics simulations, especially in studies that require ensemble sampling or crowding conditions. However, a frequent and frustrating pain point for molecular modelers arises…

When preparing a biomolecular system for simulation, one common challenge is deciding how to handle water molecules. This can be especially tricky if you want to remove excess solvent but preserve functionally important active-site waters. Removing all crystal waters by…

When creating molecular animations for presentations or publication, many researchers face a challenge: how to isolate and clearly communicate the motion of a specific part of a molecule, such as a ligand docking into a protein binding site, when the…

A common challenge in molecular modeling is figuring out how a molecule responds to external constraints or manipulations. What happens when you pull on an atom in a molecule? How does the rest of the structure adapt? Many molecular modelers…

Molecular modelers often face a recurring challenge: selecting specific atoms out of a complex structure based on well-defined criteria such as spatial coordinates, atomic types, or custom geometrical constraints. Whether preparing a region for simulation or visualizing a portion of…

Removing water molecules may seem like a straightforward preprocessing step before running a molecular dynamics simulation. However, when dealing with experimental structures such as those from the Protein Data Bank (PDB), some of the water molecules—especially those near the active…

One of the everyday challenges in molecular modeling is building customized polymers from non-standard monomer units. Whether you’re working on conjugated systems, biomaterials, or drug-polymer conjugates, chances are you need more than a basic monomer library—you need flexibility. The Polymer…

When working on molecular systems, it’s common to revisit specific parts of a structure repeatedly: a ligand, a set of residues near the active site, water molecules, binding pockets, and more. Navigating back and forth between these selections can quickly…

In molecular modeling, where precise manipulations and iterative design are crucial, accidental changes can break a workflow—or even worse, lead to unnoticed errors in a complex system. If you’ve ever altered a molecular structure and immediately regretted it, SAMSON’s history…