SAMSON Blog – Page 68

Choosing What You Click: Understand Selection Filters in SAMSON

When working on molecular systems with hundreds or thousands of atoms, fast and precise selection becomes critical. Do you really want to scroll endlessly or click around trying to highlight just the residues or atoms you care about? 🧬 In…

Running Python Scripts Directly in SAMSON

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For molecular modelers who regularly write or experiment with small scripts to automate tasks or test algorithms, dealing with external script runners can be inconvenient. Switching between your molecular design environment and a text editor or terminal can break your…

From SMILES to 3D in Seconds: An Easier Way to Generate Molecular Structures

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Turning a SMILES string into a reliable 3D molecular structure can often feel more complicated than it needs to be. If you frequently work with virtual screening, molecular docking, or QSAR modeling, you’ve likely spent too much time juggling between…

Quickly Find Chains by Atom Counts in SAMSON

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When working with complex molecular models in SAMSON, it’s easy to get lost in the layers of structural information—atoms, residues, chains, segments, and so on. For molecular modelers, one of the most time-consuming tasks can be identifying specific chains based…

Avoiding Common Pitfalls When Creating Coarse-Grained Models with Multiple Protein Replicas

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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…

Avoid Simulation Artifacts: How to Define the Box for COM Pulling in GROMACS

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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…

Let Your Molecules Talk Back: Using Voice Commands in SAMSON AI

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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…

Avoid Email Chaos: A Smarter Way to Share Molecular Files

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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…

Avoid Simulation Failures: Test Your Molecular Dynamics Setup Locally First

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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…

Making Molecular Projects Portable with File Embedding in SAMSON

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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…