OneAngstrom – Page 60

Confused About Input Files for Production MD? Here’s a Practical Guide

One of the recurring confusions among molecular modelers using GROMACS is selecting the proper input files for a production molecular dynamics (MD) simulation. This seemingly simple step can quickly become a bottleneck—especially when switching between equilibration and production phases, or…

Need to Track Atomic Movement? Try Visualizing the Center-of-Mass Pathline

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When working with molecular simulations, seeing is understanding. But if you’re analyzing ligand unbinding events, conformational changes, or diffusion mechanisms, it can be surprisingly hard to visualize how a group of atoms actually moves through space over time. Often, researchers…

Making Molecular Visuals Manageable: Using Visibility Attributes in SAMSON

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Working with complex molecular systems often means dealing with large, tangled visual representations. When atoms, residues, and molecular surfaces overlap in your viewport, even the most beautiful structures become hard to interpret. This is a common problem molecular modelers face:…

Avoiding Model Instability: How to Check if Your Energy Minimization Actually Worked

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When working with molecular systems in GROMACS, energy minimization is a critical step to eliminate steric clashes and create a geometry that’s suitable for molecular dynamics. But how can you be sure it’s actually done properly? If you’ve ever launched…

Avoid the Pain of Script-Based PMF Calculations with GROMACS Wizard

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If you’ve ever performed Potential of Mean Force (PMF) calculations using GROMACS, you probably remember the long list of scripts and careful file organization required to properly apply the Weighted Histogram Analysis Method (WHAM). Piecing together dozens of outputs from…

Quickly Isolate Segments by Atom Counts in SAMSON

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When dealing with large biomolecular systems, one of the frequent frustrations for molecular modelers is filtering and navigating through complex segment structures — especially when each segment may have hundreds or thousands of atoms. How do you swiftly locate the…

How to Keep Everything Together in Your Molecular Modeling Project

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When working on molecular modeling projects, keeping track of all relevant files—input data, Python scripts, images, papers, notes—can become challenging. Files are often scattered across folders or hard drives, shared by email, or lost in different versions. Wouldn’t it be…

Exploring the Role of Defects in Diamond Structures

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Defects in crystals are not just imperfections—they are the key to understanding and designing materials with advanced properties. If you’re working with molecular models and wondering how to explore atomic-scale imperfections in diamond—one of the most iconic crystals—this post offers…

From FASTA to 3D: Predict Protein Structures with AlphaFold-2 in SAMSON

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Predicting protein structures has become much more accessible thanks to tools like AlphaFold-2. However, setting up a structure prediction pipeline and visualizing results can still demand considerable effort—especially for those new to computational biology or looking to streamline their workflow.…

Making Your Molecular Projects Self-Contained with Embedded Files and Folders

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One common frustration among molecular modelers is managing all the files that come with a single project: molecular structures, datasets, reference PDFs, scripts, and more. Moving your project to another computer or sharing it with collaborators can quickly become messy…