SAMSON Blog – Page 75

Quickly show or hide molecular elements using NSL’s presentation attributes

Molecular modelers often manipulate large, complex systems composed of many structural and visual elements. Whether you’re highlighting specific atoms for analysis or preparing a figure for publication, controlling the visibility of these elements is essential. However, manually toggling visibility through…

Avoid Drifting Ligands: Proper Energy Setup in Ligand Unbinding Simulations

OneAngstrom

When exploring ligand unbinding pathways in molecular modeling, one common frustration is the unrealistic movement of either the ligand or the protein during simulations. If you’ve found your protein drifting along with the ligand or noticed unnatural trajectories, the problem…

Tired of Switching Between Tools? Here’s How You Can Integrate Your Workflow in SAMSON

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Molecular modelers often face the challenge of jumping between different tools and platforms to complete different parts of their workflows. Running an optimization in one tool, visualizing it in another, and writing custom scripts to connect them can slow down…

Local GROMACS Simulations Without Slowing Down Your Computer

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Running molecular simulations can be demanding on your computer, especially when using software like GROMACS. If you’ve ever tried to run a local job and found your system nearly unusable during the simulation, you’re not alone. This is a common…

Tired of Losing Molecular Motion Details? Try This Simple Recording Trick

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When creating molecular presentations or simulations, one common frustration among researchers and modelers is realizing that the changes in atomic positions — carefully crafted through movements, docking steps, or simulations — are not thoroughly documented or not reproducible when returning…

Which Unit Cell Should You Choose for Periodic Boundary Conditions?

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When performing molecular simulations with periodic boundary conditions (PBC) in GROMACS, one subtle choice can have a measurable impact on both the accuracy and efficiency of your results: the shape of the unit cell. If you’ve ever wondered whether to…

Avoid Sampling Pitfalls: How to Set Up a Ligand for Pathway Discovery

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One common challenge in computational molecular design is correctly preparing a protein-ligand system for dynamic simulations. Poor initial setup can lead to unusable results or misleading data, especially when exploring ligand unbinding pathways. In this post, we focus on a…

Filtering Structural Groups by Partial Charge in SAMSON

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When working with molecular models and simulations, it’s often important to quickly locate molecular fragments with specific electronic characteristics. One common use case: identifying structural groups with a particular range of partial charges — whether for reactivity analysis, parameter tuning,…

Previewing Protein Symmetry in Real Time Without Committing

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When working with crystallographic or biological assemblies of proteins, understanding how subunits are arranged is essential. Whether you’re modeling quaternary structures or designing symmetric nanostructures, replicating and visualizing symmetric interfaces can be a key step. But generating all symmetry mates…

Setting Up a Coarse-Grained MD System in Seconds: A Practical Guide for Soluble Proteins

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For many molecular modelers, setting up coarse-grained (CG) molecular dynamics (MD) systems can be a tedious and error-prone task. Between topology generation, solvation, ion addition, and force field configuration, it’s easy to get stuck in a series of manual steps…