OneAngstrom – Page 232

Running GROMACS Simulations in the Cloud without the Setup Stress

For molecular modelers, one recurring challenge is ensuring enough computational power to run molecular dynamics simulations efficiently. This becomes especially pressing when working with large systems or when comparison between multiple parameter combinations is needed. Local machines often fall short,…

Center, Align, Repeat: Making Molecules Line Up in SAMSON

OneAngstrom

If you’ve ever worked with complex molecular arrangements, you know how easy it is to end up with atoms scattered all over your viewport. Whether you’re preparing a clean scene for publication, building a supramolecular assembly, or simply organizing a…

Selective Deletion of Water Molecules in Molecular Simulations: A Simple Strategy

OneAngstrom

When preparing biomolecular systems for molecular dynamics using GROMACS, one frequent challenge is deciding which water molecules to retain. Automatically removing all crystallographic water may affect the behavior of key biological sites, especially if some of these water molecules are…

Making the Most of Sequence Alignments by Selecting Residues in SAMSON

OneAngstrom

When comparing protein structures, molecular modelers often need to go deeper than a global superposition. Understanding how specific residues align across different proteins or chains can be critical for identifying conserved sites, mapping functional regions, and guiding mutation or ligand…

Visibility, Selection, and Filtering: A Smarter Way to Navigate Molecular Animations

OneAngstrom

Working with molecular animations can quickly become overwhelming within large and complex systems. Whether you’re visualizing conformational changes, analyzing dynamic interactions, or simply presenting molecular scenes, clarity is crucial. One common pain for modelers is managing what you see —…

Spend Less Time Rearranging Panels and More Time Modeling Molecules

OneAngstrom

Molecular modelers often spend long hours analyzing structures, running simulations, and visualizing results. A common and frustrating pain point? Wasted time rearranging software interfaces, hunting for tools, or trying to recreate the same setup with every new session. Fortunately, the…

Finding Charged Amino Acids in Large Systems: A Simple and Powerful Filter

OneAngstrom

When exploring large biomolecular structures in molecular modeling, one of the frequent needs is identifying specific residues by their chemical properties. Whether refining a force field, preparing an input file, or designing a mutation experiment, knowing exactly where the positively…

Synchronizing Molecular Trajectories with Play Path: A Simple Way to Review Dynamic Changes

OneAngstrom

One of the most common challenges in molecular modeling is reviewing and presenting dynamic changes across different conformations or simulations. Whether you’re studying protein folding, ligand docking, or large-scale molecular motions, being able to visualize changes smoothly over time is…

Filtering Molecular Structures by Partial Charge in SAMSON

OneAngstrom

For computational chemists and molecular modelers, screening structural groups based on charge is often key to understanding reactivity, electrostatics, or guiding docking simulations. But quickly identifying molecular groups based on total partial charge in a large system can be cumbersome…

From Simulation to Story: Creating Molecular Animations with SAMSON’s Animator

OneAngstrom

Have you ever struggled to share the results of your molecular simulations or structural analyses in a way that truly captures the complexity of what you’re studying? Static images can be useful, but they often fall short when it comes…