SAMSON Blog – Page 279

Running Molecular Dynamics Simulations in the Cloud with GROMACS Wizard

Running molecular dynamics (MD) simulations with GROMACS can be resource-intensive, particularly when working with large systems or long time scales. If you’ve ever been limited by computational power on your local machine — or had to abandon simulations partway through…

Why Named Cameras Can Save You Hours in Molecular Modeling Projects

OneAngstrom

When working on complex molecular systems in SAMSON and building dynamic scenes with multiple views, it is not unusual to end up with several camera nodes storing different viewpoints. A common frustration among molecular modelers is locating the right camera…

Two Ways to Add Atoms in SAMSON (and When to Use Each)

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When you’re building molecular structures from scratch, particularly for custom molecules or intermediates, the process often starts with adding atoms one by one. In SAMSON, there are two primary ways to do this — and both offer distinct benefits depending…

Controlling the Pace of Molecular Animations with Pause Frames

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When creating molecular animations, one recurring challenge is controlling viewer focus. Things move fast—sometimes too fast. You might be trying to highlight a conformational change, emphasize a binding event, or pause at a molecular interaction that deserves more attention before…

Struggling With GROMACS Index Groups? Here’s a Simple Way to Manage Them Visually

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Creating and managing index groups in GROMACS can be tedious, especially when working with large biomolecular systems. Whether you’re setting up pulling groups, defining restraints, or preparing simulations, it often requires command-line scripts or careful hand-editing of selections. Fortunately, there’s…

Choosing What to Import After Your NVT Equilibration

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After running molecular dynamics simulations, especially in tools like the GROMACS Wizard in SAMSON, a common question arises: What exactly should I import from my simulation? This may seem like a simple decision, but it can impact your analysis workflow…

A Quick Way to Align Molecular Structures in SAMSON

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Aligning molecular structures can be a repetitive task in molecular modeling, especially when working with multiple structures or preparing publications and interactive presentations. Minor misalignments can have a noticeable impact on how data is interpreted. But if you’re using SAMSON,…

Easily Select Residues Based on Charge and Polarity in SAMSON

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Working with complex biomolecular structures often requires isolating specific types of residues, such as those that are charged or hydrophobic. This task frequently arises in molecular modeling workflows—whether you’re designing mutations, analyzing ligand binding, or preparing systems for simulations. In…

A Simple Way to Validate Protein Structures Using Symmetry

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When modeling large biological assemblies like viral capsids or multimeric protein complexes, a frequent question is: does this structure actually make sense? Symmetry can be a powerful clue. Many biological assemblies exhibit some form of symmetry—cyclic (Cn), dihedral (Dn), or…

Reducing Docking Time with Smarter Search Domain Setup in Hex

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One of the most common challenges in protein-protein docking is the trade-off between accuracy and computational time. A full rotational search in docking can be very intensive, especially when you’re screening multiple systems or tweaking parameters. Fortunately, if you already…