Author: OneAngstrom

Simulating systems with multiple copies of a protein—such as membrane-bound proteins or protein condensates—is common in molecular modeling. Coarse-graining these systems using MARTINI force fields can significantly accelerate simulations, but there’s a critical step that often causes confusion: handling multiple…

When running a center-of-mass (COM) pulling simulation in molecular dynamics, one critical and often overlooked step is setting the simulation box size appropriately. Without enough space in the pulling direction, your simulation can suffer from periodic boundary artifacts, invalidating results…

If you’ve ever wished you could talk to your molecular modeling software and have it respond with actions, that moment has arrived. One of the lesser-known but surprisingly handy features of SAMSON AI, the intelligent assistant integrated into the SAMSON…

One of the recurring frustrations for molecular modelers is trying to collaborate efficiently with peers. Whether you’re sharing molecular designs, simulation input files, or results with a colleague, supervisor, or an entire team, the typical exchange happens over long email…

Running molecular dynamics simulations—especially in the cloud—can consume both time and computational credits. For researchers using SAMSON’s GROMACS Wizard, launching a simulation in the cloud is surprisingly easy. However, when something goes wrong during a run, troubleshooting can be frustrating…

Keeping all your data organized and portable is one of the recurring challenges in molecular modeling. Whether you’re working on protein-ligand simulations, sharing results with collaborators, or archiving your work for future reference, one thing is certain: jumping between multiple…

Understanding how a protein transitions between conformations is a key goal in structural biology. While computational tools for finding these paths exist, researchers frequently struggle with an important practical question: how can we export and visualize these conformational transitions in…

One of the most common challenges in molecular modeling lies in **polymer customization**. You might have specific monomer units you want to connect or test, but lack a visual, structured, and flexible way to define them before building full polymer…

When setting up coarse-grained (CG) molecular dynamics simulations using the MARTINI force field, one recurring roadblock for molecular modelers is handling multiple replicas of the same protein. Whether you’re modeling crowded cellular environments or testing multimeric assemblies, creating multiple instances…