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Preparing and running molecular dynamics (MD) simulations locally often requires significant setup: installing packages, managing dependencies, compiling code, setting up GPUs and CPUs, and more. For many molecular modelers, this overhead is frustrating—especially when it takes more time to set…

When working on complex molecular models, one recurring challenge is managing the visual navigation across different regions of interest. Whether you’re alternating between atomic-scale details and global structure overviews, or inspecting interactions from different angles, jumping around in 3D space…

Molecular modelers often rely on precise control over their simulation environments — for reasons ranging from reproducibility to compatibility with previous work or external tools. One recurring issue is being forced to use a default GROMACS version bundled within software,…

For many molecular modelers, running large-scale GROMACS simulations is limited by local computing power. Long simulations, memory-heavy systems, or multiple production runs for enhanced sampling can all push the limits of a typical workstation. Cloud computing has emerged as a…

When preparing molecular simulations in GROMACS, one common need among computational researchers is the ability to define precise groups of atoms or residues—whether for analysis, distance restraints, pull groups, or umbrella sampling setups. While GROMACS offers native tools like gmx…

If you’re working with molecular dynamics simulations, chances are you’ve used GROMACS, a powerful and widely used MD engine. SAMSON’s GROMACS Wizard makes it easy to run GROMACS computations, both locally and in the cloud. But what if you need…

Running a molecular dynamics (MD) simulation is only half the story. For many molecular modelers, the real challenge comes after: importing the results, making sense of them, and preparing overview plots to check simulation health or communicate findings. If you’ve…

When working with protein structures from the Protein Data Bank (PDB), modeling biological assemblies usually requires rebuilding symmetry-related units based on transformation matrices encoded in the structure file. This can often be a tedious task — and yet it’s essential:…

Energy minimization is a critical step in preparing molecular systems for simulations, ensuring that your model is stable and ready for further refinement. But for many molecular modelers, especially those working with personal computers, a common problem arises: How do…