SAMSON Blog – Page 232

When and How to Minimize Ligands Before Docking with AutoDock Vina Extended

One of the most overlooked steps in molecular docking workflows is the proper preparation and minimization of ligands. While skipping this step might seem tempting—especially when working with large ligand libraries—it can significantly affect docking results, particularly when ligands are…

Quickly Identify Side Chains by Name, Charge, Size and More

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If you’re modeling biomolecular systems, navigating large molecules to find specific side chains with certain characteristics can be time-consuming. Whether you’re optimizing a binding site, running electrostatics calculations, or preparing a molecule for coarse-grained simulations, filtering side chains by their…

Selecting Atoms Like a Pro in SAMSON: An Introduction to NSL

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When working with complex molecular systems, selecting atoms for visualization, editing, or analysis can quickly become overwhelming. Whether you’re developing a new molecule, importing data from experimental studies, or running simulations, you’ll often need to isolate parts of a system—like…

Stop Searching for Files: Streamline GROMACS Input Selection with Auto-Fill

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Anyone working with molecular simulations knows the frustration of constantly navigating folders to locate the correct input files—especially when transitioning between simulation steps like energy minimization, NVT equilibration, and NPT equilibration. If you’re using the GROMACS Wizard in SAMSON, there’s…

Effortlessly Identify Hydrogen Bond Donors and Acceptors in Your Molecular Models

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When modeling molecular systems, identifying hydrogen bond donors and acceptors quickly and accurately is often crucial. Whether you’re preparing structures for docking, analyzing interactions in a protein-ligand complex, or filtering atoms for visualization, being able to specify which atoms participate…

Quickly Find Specific Chains Using NSL in SAMSON

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If you’re working with large biomolecular systems in SAMSON, it can become overwhelming to manage and analyze specific chains. Whether you’re editing, visualizing, or preparing systems for simulations, refining your selection to just the relevant molecular chains can save significant…

Avoiding Periodic Pitfalls: Setting Up the Box for COM Pulling in Molecular Simulations

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When setting up a molecular dynamics (MD) simulation involving pulling, a frequent source of frustration among researchers is improper definition of the simulation box. The consequences? Artifacts due to periodic boundary conditions — from nonphysical interactions to misleading energy profiles.…

Filtering Aromatic Atoms, the Smart Way

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Working with aromatic systems is an essential part of structure-based molecular modeling, from visualizing planar ring systems to performing conformational analysis on drug-like molecules. But selecting these atoms precisely can be time-consuming—especially when your molecules are large or complex. This…

Why Run GROMACS Simulations in the Cloud?

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If you’ve ever run molecular dynamics simulations with GROMACS, you already know how demanding they can be in terms of computational resources. Long trajectories, multiple replicas, and fine-grained time steps can push even powerful workstations to their limits. But what…

Making Molecules Appear at Just the Right Moment

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It’s a familiar scenario for many molecular modelers preparing visual presentations: you’re building a molecular animation and want specific atoms, molecules, or protein subunits to appear smoothly at a precise point in time. You don’t want them to fade in…