OneAngstrom – Page 76

Creating Custom GROMACS Index Groups Without the Headaches

When working with molecular dynamics simulations in GROMACS, one common challenge is defining atomic groups for analysis, restraints, or pull codes. By default, GROMACS generates some standard index groups (like Protein, Water, or Ion) automatically. But what if you need…

Quickly Find Molecular Segments by Atom Counts or Charges in SAMSON

OneAngstrom

If you work with complex molecular systems, you’ve probably encountered situations where you needed to quickly focus on specific parts — for example, all segments with more than 500 atoms, or those containing a certain number of carbon atoms. SAMSON’s…

How to Safely Customize Atom Typization When Using UFF in SAMSON

OneAngstrom

When running simulations with the Universal Force Field (UFF) in SAMSON, molecular modelers often seek the flexibility to fine-tune atom types, bond orders, or valences. While UFF does a good job at automatically perceiving this information, there are cases—especially when…

What Happens If You Forget to Save Your Molecular Measurements?

OneAngstrom

Many molecular modelers have shared the same frustrating experience: measuring a distance or angle between atoms in a molecular system, only to realize that the value disappeared moments later. What’s going on here? In SAMSON, molecular measurements like bond lengths,…

How to Correctly Define a Simulation Box for COM Pulling

OneAngstrom

When preparing molecular dynamics simulations that involve center-of-mass (COM) pulling — such as separating chains in a protein complex — one of the most common sources of error is the incorrect definition of the simulation box. The consequences? Unexpected interactions…

Trouble Seeing Labels in Your Model? Here’s a Precise Way to Control Visibility

OneAngstrom

When working with complex molecular designs in SAMSON, it’s easy to lose track of labels—especially when shifting between different states, selections, or visualization settings. If you’ve ever had the frustrating experience of wondering why a label isn’t visible (or why…

Changing Simulation Parameters Without Breaking Your Workflow

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If you’ve ever felt the friction of customizing molecular dynamics (MD) simulations in GROMACS, you’re not alone. Manually editing .mdp files, searching for the right flags, worrying about compatibility—all of this can slow down your work and distract you from…

Filtering Molecular Paths by Atom Count in SAMSON

OneAngstrom

When working with complex molecular models, it’s common to want to isolate specific structural paths—like chains, ligands, or pathways—that meet certain criteria. One frequent need is to find paths based on their size, that is, the number of atoms they…

Choosing Initial Conformations for Umbrella Sampling Without Guesswork

OneAngstrom

Setting up an umbrella sampling simulation can be a tedious process, especially when trying to decide which snapshots to use as initial conformations. Molecular modelers often find themselves manually selecting frames from trajectories or trying to estimate proper spacing between…

Making Sense of Bond Types in Molecular Models (Without the Guesswork)

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When you’re inspecting or designing molecular systems, it’s easy to overlook how deeply bond types influence molecular behavior. Whether you are analyzing a drug molecule, building a polymer, or examining a crystal structure, the type of bond—single, double, aromatic, and…