SAMSON Blog – Page 525

From Fragment to Function: Registering Custom Monomers in SAMSON

Designing specific polymer architectures often starts with one fundamental step: defining your own monomers. For molecular modelers working on custom polymers, functionalized scaffolds, or bioconjugates, creating a library of reusable, well-defined repeat units can streamline workflows and minimize errors later…

A Quick Guide to Selecting Render Presets in Your Molecular Models

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When working on complex molecular models, a common frustration is navigating through multiple visual states and trying to consistently control how parts of your model are rendered. If you’ve ever wished you could quickly select or filter different rendering configurations…

Controlling GROMACS Performance at Home: Thread Management Made Easy

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When molecular modelers simulate complex systems with GROMACS, performance often becomes a bottleneck — especially on local machines. Whether you’re testing a new protocol or running multiple small systems, getting the most out of your processor can make the difference…

Can’t Open a Molecular File? Here’s What You Can Do in SAMSON.

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One of the most common frustrations in molecular modeling is trying to open a file, only to be told that the format is not supported. Whether it’s a .pdb, .xyz, a cryo-EM density file, or something less common, not being…

Aligning Molecules Made Simple: A Visual Overview in SAMSON

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Precise manipulation of molecular structures is a core task in molecular modeling. Whether you’re preparing models for simulations, visualizations, or comparative studies, structural alignment plays a vital role. Yet, aligning molecules accurately in 3D space can be time-consuming if the…

Avoid Common Pitfalls When Launching NPT Equilibration in GROMACS Wizard

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NPT equilibration is a critical step in molecular dynamics simulations. It’s the phase where your system stabilizes at the desired pressure and density, and skipping or misconfiguring this step can lead to inaccurate results downstream. Fortunately, GROMACS Wizard in SAMSON…

Setting Up a Protein for Conformational Path Sampling: What You Might Be Skipping

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Before diving into modeling the dynamic transitions of proteins, there’s one crucial step that often gets overlooked – correctly preparing your molecular systems. This seemingly simple process can make or break the results you get from advanced tools like the…

A Simpler Way to Catch Strained Residues Before Simulation

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One of the ongoing challenges in molecular modeling is making sure protein structures are valid enough for simulation. Protein refinement workflows often reveal residues that don’t quite fit the geometric or energetic expectations—outliers in backbone conformation. These strained residues can…

Launching Molecular Dynamics Simulations in the Cloud with GROMACS Wizard

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Running molecular dynamics (MD) simulations can be computationally intensive, especially for large systems. This often limits researchers to what their local hardware can handle, or forces them to navigate complex HPC systems. If you’re a molecular modeler looking for a…

Saving Time on Umbrella Sampling PMF Analysis with WHAM in SAMSON

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Performing umbrella sampling simulations is a common task in molecular modeling when estimating the Potential of Mean Force (PMF) along a reaction coordinate. But what often frustrates modelers is how cumbersome post-processing can become. Collecting the simulation outputs, ensuring consistency…