OneAngstrom – Page 55

Tweaking Bonds and Atom Types in UFF Simulations: What You Should Know

One of the recurring challenges in molecular modeling is ensuring that force field parameters truly reflect the intent behind your molecular system. Whether you’re refining a biomolecule or designing a novel compound, automatic parameterization tools can’t always know exactly what…

A Simple Trick to Record Trajectories for Molecular Presentations in SAMSON

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When building molecular presentations or animations in SAMSON, there often comes a moment when you wish to record how atoms move—either to show a docking process, a simulation, or a molecular rearrangement. But manually tracking trajectories frame by frame? That’s…

Avoid Manual File Errors: Selecting Input Structures in NPT Equilibration

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One common source of frustration in molecular dynamics workflows is accidentally using the wrong input file when transitioning between simulation stages. This becomes especially problematic during equilibration steps where mismatches can cause runs to crash or yield incorrect results. In…

Exporting Molecular Structures from SAMSON: What You Need to Know

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When working on molecular modeling projects, exporting your results into the right file formats is a crucial step—whether you’re preparing datasets for collaborators, submitting to databases, or moving your models into other software tools. However, choosing the appropriate exporter, and…

Step-by-step approach to building a nanotube manually

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Designing nanoscale structures like carbon nanotubes (CNTs) is a common task in nanotechnology and materials science, yet can be time-consuming using traditional modeling tools. One of the most frequent pains reported by molecular modelers is the difficulty in manually assembling…

From Fragment to Function: Registering Custom Monomers in SAMSON

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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…