SAMSON Blog – Page 109

Streamline Protein Cleanup: Batch Preparation Made Simple

Anyone working with molecular models knows the slow drip of time lost to repetitive cleanup tasks: removing waters, deleting unwanted ligands, fixing missing atoms, and ensuring the structure won’t crash a simulation. It’s manageable when working with one or two…

Finding Molecular Backbones by Property in SAMSON

OneAngstrom

When working on complex molecular models, it’s common to ask very specific questions about a particular system: How many backbone groups have a partial charge above a certain threshold? Which ones are invisible or lack material? Are there backbones with…

Preparing Dozens of Protein Structures? Try This Workflow-Saving Tool

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If you’ve ever had to prepare a large number of protein structures for simulations or docking runs, you know how time-consuming it can be to check alternate locations, add missing atoms, strip solvents, and standardize formats—file by file. Whether you’re…

Changing Atom Attributes Without Breaking Your Model

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One of the recurring challenges faced by molecular modelers is fine-tuning the structural details of their models without introducing inconsistencies. Whether you’re adjusting atomic positions, types, or making minor corrections in a structure, you often want surgical precision over your…

Let Keyframes Do the Hiding: A Simple Way to Control Molecular Visibility in SAMSON

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In molecular modeling, presenting a complex mechanism often requires temporarily hiding parts of a molecular system to direct attention. For example, a protein’s active site might be buried deep within a folded structure. To highlight its dynamics, it helps to…

Using GROMACS Performance Parameters Without Overloading Your System

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Running molecular dynamics simulations can be demanding on your hardware. It’s common to see users overwhelmed by lagging systems or jobs that fail due to poor performance settings. If you’re using GROMACS Wizard in SAMSON, there’s a simple way to…

Quickly Select Charged or Polar Residues Using NSL in SAMSON

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Imagine you’re preparing to simulate a protein in a new solvent environment. One of the first steps is deciding which residues might interact more strongly with the environment—perhaps charged residues for pH-sensitive behavior, or polar residues for solvent-accessible surface analysis.…

Making the Most of Idle Time: Run GROMACS Simulations in the Cloud

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Molecular dynamics (MD) simulations can be time-consuming, especially when you’re working with larger systems or limited local computational power. For many molecular modelers, long simulations mean one thing: your workstation becomes unusable for hours, or even days. Luckily, SAMSON GROMACS…

How to Quickly Select Molecular Paths with a Specific Number of Atoms in SAMSON

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When dealing with complex molecular systems, it’s often necessary to focus on specific parts of a model to streamline analysis or editing. For example, you might want to target all molecular paths with more than 100 atoms for further inspection,…

Avoid Chain Conflicts When Generating CG Models with Martinize2

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When working with coarse-grained (CG) molecular models, it’s common to simulate multiple copies—or replicas—of the same protein in a single system. This setup is especially useful for studies involving protein aggregation, diffusion, or encapsulation. However, many researchers new to coarse-graining…