OneAngstrom – Page 50

Synchronizing Your Views: A More Intuitive Way to Work with Molecular Sequences

For many molecular modelers, managing complex biomolecular systems means jumping between multiple representations: 3D structures, sequences, and data tables. A frequent source of friction is the disconnect between these representations—particularly when selecting elements in one view doesn’t immediately reflect in…

How to Create Custom Index Groups in GROMACS Wizard Without Writing a Line of Code

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When running advanced molecular dynamics simulations, especially those involving pull groups or complex post-simulation analysis, it’s often necessary to define custom index groups. This is typically done using gmx make_ndx, which requires knowledge of GROMACS command-line syntax and selection strings.…

When Steepest Descent Isn’t Enough: Accelerating Molecular Relaxation with FIRE

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Geometry optimization is an essential step in molecular modeling workflows, whether you’re preparing initial configurations for simulations or cleaning up experimental structures. But if you’ve ever felt that your steepest descent minimizer just isn’t converging fast enough—especially in systems with…

Make sense of molecular visualizations by filtering visible nodes in SAMSON

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If you’ve ever worked on a large molecular system, you know how cluttered the visual scene can become. Whether you’re analyzing docking results, molecular dynamics trajectories, or assembling molecular systems, excessive visual complexity often slows down interpretation and leads to…

Avoid Solvent Clashes in Coarse-Grained MD Simulations by Adjusting van der Waals Distances

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One common frustration for molecular modelers preparing coarse-grained (CG) systems for molecular dynamics simulations is dealing with solvated structures where solvent beads overlap with solute atoms. These clashes often cause failed simulations or unphysical behavior. The root cause? The default…

A Practical Guide to Covalent Docking with the FITTED Suite in SAMSON

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Covalent docking is a powerful strategy in structure-based drug design, especially when targeting active sites with known reactive residues. However, setting things up properly — from hybridization to binding site specification — can be a major source of friction for…

Got a GROMACS Trajectory? Here’s How to Use It for Umbrella Sampling in One Go

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Umbrella Sampling is a powerful technique for calculating free energy profiles along reaction coordinates, but setting it up can be time-consuming, especially when using data from existing trajectories. If you’re a molecular modeler with a finished GROMACS trajectory from a…

Why Your Molecular Simulations May Fail Without NVT Equilibration

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One of the most common frustrations that molecular modelers encounter is when a simulation runs, but the system behaves erratically—either heating up quickly or displaying unstable behavior. A major reason? Skipping or misconfiguring the NVT equilibration phase. In molecular dynamics,…

Target Specific Atoms by Geometry in SAMSON: A Practical Guide for Molecular Modeling

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One of the recurring challenges in molecular modeling is selecting atoms based on structural properties – particularly geometry. For instance, identifying atoms with tetrahedral geometry can be important for understanding chemical reactivity, assigning force field parameters, or preparing input for…

Make Models Fade Naturally with the Disappear Animation in SAMSON

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In molecular modeling, visual clarity is key. Whether you are preparing educational content, publishing research, or just trying to better understand a complex structure, being able to control what appears and disappears from your view can make a big difference.…