OneAngstrom – Page 125

Pausing Molecular Presentations at Just the Right Moment

Molecular modeling often involves complex, dynamic simulations where every second counts — literally. When giving a molecular presentation or preparing an animation of a simulation, highlighting specific structural changes at the exact moment they occur can greatly enhance understanding. But…

Easily Find Complex Molecular Systems Using Folder Attributes in NSL

OneAngstrom

When working with large molecular systems, structural models can become very complex — from polymers with multiple chains and residues to assemblies containing thousands of atoms. As your project grows, finding specific parts of your dataset can become difficult and…

How to Control GROMACS Thread Usage in SAMSON Without Slowing Down Your Computer

OneAngstrom

If you’ve ever tried to simulate a molecular system locally using GROMACS and noticed your entire system becoming sluggish—or worse, freezing—you’re not alone. Molecular dynamics simulations are computationally intensive, and unless configured properly, they can push your CPU to its…

Avoiding Topology Errors When Creating Protein Replicas in SAMSON

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Working with multiple replicas of a protein system is common practice when setting up coarse-grained (CG) molecular dynamics simulations, especially in studies that require ensemble sampling or crowding conditions. However, a frequent and frustrating pain point for molecular modelers arises…

Preserving Active-Site Waters in Molecular Simulations

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When preparing a biomolecular system for simulation, one common challenge is deciding how to handle water molecules. This can be especially tricky if you want to remove excess solvent but preserve functionally important active-site waters. Removing all crystal waters by…

Fixing Atoms to Clarify Molecular Motion

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When creating molecular animations for presentations or publication, many researchers face a challenge: how to isolate and clearly communicate the motion of a specific part of a molecule, such as a ligand docking into a protein binding site, when the…

Dragging Atoms, Rebuilding Molecules: A Look at Interactive Molecular Simulation in SAMSON

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A common challenge in molecular modeling is figuring out how a molecule responds to external constraints or manipulations. What happens when you pull on an atom in a molecule? How does the rest of the structure adapt? Many molecular modelers…

Selecting Atoms with Precision Using Mathematical Expressions

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Molecular modelers often face a recurring challenge: selecting specific atoms out of a complex structure based on well-defined criteria such as spatial coordinates, atomic types, or custom geometrical constraints. Whether preparing a region for simulation or visualizing a portion of…

Efficiently Selecting Cameras in SAMSON Using NSL

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When working on complex molecular scenes in SAMSON, camera nodes can quickly accumulate. You might create a camera for each important orientation, set up different annotation views, or manage several visualization perspectives in parallel. Over time, finding and managing the…

When (and How) to Remove Crystal Waters Before Simulation

OneAngstrom

Removing water molecules may seem like a straightforward preprocessing step before running a molecular dynamics simulation. However, when dealing with experimental structures such as those from the Protein Data Bank (PDB), some of the water molecules—especially those near the active…