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Avoid Equilibration Errors: Choosing the Right Input for NVT in GROMACS Wizard

If you’ve ever found yourself scratching your head because your molecular dynamics simulation didn’t behave as expected during the NVT equilibration phase, you’re not alone. One of the most common causes? Incorrect or inconsistent input files. Choosing the correct starting…

Targeting Specific Residues in Your Molecular Models with NSL

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If you’re working on complex biomolecular systems, there’s a good chance you’ve needed to focus on a specific subset of residues — perhaps only charged amino acids, those in beta sheets, or ones located at sequence termini. Filtering and selecting…

Quickly Find Molecular Conformations Based on Atom Count in SAMSON

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If you’re a molecular modeler working with large datasets of conformations, you’ve probably encountered the challenge of finding specific structures within big systems. Whether you’re screening generated conformations or preparing simulations, it’s often important to filter models based on the…

Maintain a Consistent Viewpoint in Molecular Movies with ‘Hold Camera’

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When building scientific presentations or molecular animations, there’s often a need to maintain a specific viewpoint of a system across several frames. This is particularly true when showcasing the progression of a simulation, comparing different ligand dockings, or simply keeping…

From design to simulation: exporting DNA nanostructures in Adenita

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One of the most common challenges DNA nanostructure designers face is transitioning from visual design to simulation. Creating a structure is just the beginning — taking it to analysis or dynamics studies in simulation tools like oxDNA or using sequence…

A Molecular Modeler’s Guide to Smooth Camera Paths in SAMSON

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Creating compelling molecular animations often comes down to capturing the right movement of the camera. If you’ve ever struggled to create smooth, controlled camera transitions when presenting your molecular models, you’re not alone. It’s a common challenge for researchers and…

Faster Molecule Cleanup: Precision Visibility Filtering in SAMSON

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When working on complex molecular systems, molecular modelers often face visual clutter—overlapping structures, excessive representations, or simply too much visual data to intuitively understand what’s happening. SAMSON, the integrative platform for molecular design, offers a practical solution to this challenge…

How to Monitor and Manage Your Cloud Simulations in SAMSON

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For molecular modelers running simulations with GROMACS in the cloud through the SAMSON GROMACS Wizard, a recurring concern is visibility and control. What happens after submitting a job? How can one monitor progress, pause, or cancel a simulation if something’s…

Managing Extensions in SAMSON: Customizing Your Molecular Modeling Workspace

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Molecular modeling often demands very different tools depending on the type of task—a structural biologist, a materials scientist, and a quantum chemist may all use different workflows. This diversity in needs can lead to cluttered or inefficient software environments that…

Trouble Selecting Atom Groups in GROMACS? Here’s a Faster Way with SAMSON

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For molecular modelers working with GROMACS, creating custom index groups can be a valuable but time-consuming step, especially when setting up umbrella sampling or applying restraints to specific parts of a biomolecular system. While GROMACS provides the gmx make_ndx command…