SAMSON Blog – Page 194

Quickly Filter Conformations by Atom Count in SAMSON

When working with complex molecular systems in SAMSON, molecular modelers often deal with large sets of conformations. These may include snapshots from simulations, different poses from docking, or generated conformational ensembles. However, identifying conformations that meet specific structural criteria—like having…

When a Cube Isn’t the Best Fit: Choosing Space-Filling Unit Cells for Molecular Simulations

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When preparing a molecular dynamics simulation, one often-overlooked but important decision is the shape of the unit cell used for applying periodic boundary conditions. This decision can impact both the accuracy and performance of your simulation. If you’ve ever wondered…

Avoiding Common Mistakes When Choosing MD Parameters in GROMACS Wizard

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Deciding on parameters for a production molecular dynamics (MD) simulation can be one of the most deceptively time-consuming tasks in computational molecular modeling. The settings you choose—such as the number of steps, the time step size, and coupling constants—can significantly…

Switching GROMACS Versions Without Breaking a Sweat

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Many molecular modelers rely on GROMACS for running molecular dynamics simulations. It’s fast, robust, and widely used. However, there’s one issue that pops up often: how to use your specific version of GROMACS from within another platform or software like…

Working with Molecular File Formats in SAMSON: What You Need to Know

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One of the most frequent challenges in molecular modeling is dealing with incompatible file formats. Whether you’re preparing a system for simulation, analyzing results, or sharing data with collaborators, you’ve likely faced the annoyance of having to convert files or…

A Clearer Start: Making Molecular Models Appear Smoothly

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For molecular modelers and structural biologists working with complex molecular systems, presenting molecules in a clear and digestible way can be a real challenge—especially when you’re trying to guide an audience through a process, a mechanism, or a sequence of…

Filtering Molecules by Partial Charge: A Time-Saving Tip in SAMSON

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When working with complex molecular systems, identifying molecular fragments or structural groups with specific electrostatic properties can be a crucial step — whether you’re designing new molecules, setting up simulations, or analyzing charge distributions. This becomes especially relevant when you…

Working on Just One Molecule? Here’s How to Minimize Precisely in SAMSON

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If you’re modeling molecular systems with multiple molecules, you’ve probably encountered this issue: you want to fine-tune a single molecule or part of it without affecting the rest of your system. Maybe you’re adjusting a ligand conformation in a protein-ligand…

Set Your View in Molecular Videos: Using Hold Camera in SAMSON

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If you’ve ever created molecular presentations or movies, you’ve likely encountered this common issue: your molecules look exactly right in one frame and completely off in the next. This is especially true when animations are missing camera transitions or your…

Tired of Preparing Protein Structures One by One?

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If you’ve ever handled multiple PDB files, you know the pain of preparing them one at a time before a molecular modeling workflow. Manually opening each structure, checking for alternate locations, removing waters or ions, and adding hydrogens can easily…