One of the common challenges in molecular modeling is ensuring that a newly created structure is physically realistic. Molecules built manually or imported from other software often start in high-energy, non-equilibrium configurations. This can distort simulations and affect downstream analyses…

When working with molecular simulations, one of the most frequent causes of downstream issues is improperly prepared structural data. Whether you’re building coarse-grained models, simulating protein-ligand interactions, or setting up molecular dynamics runs, small inconsistencies in your input structures—like alternate…

Creating compelling molecular visualizations is an essential part of communicating molecular mechanisms, whether you’re preparing presentations, producing educational videos, or designing research figures. But there’s a frequent challenge molecular modelers face: how do you smoothly reveal or hide parts of…

When molecular modelers present complex systems, it’s essential to maintain clear, consistent visual perspectives. During animations—whether for presentations, simulations, or teaching—you may want to move the camera along a horizontal path, preserving orientation while scanning across a molecular structure. SAMSON’s…

When preparing animated molecular presentations, a common challenge researchers face is visualizing how atoms or molecules move across time. Just watching the animation may not give enough insight into the exact path atoms follow. This can be critical, especially when…

Defining custom index groups can often be one of the trickiest steps for molecular modellers when setting up pulling simulations in GROMACS. If you’re performing center-of-mass (COM) pulling, it’s crucial that the pulled and reference groups are properly defined. In…

Protein modeling often runs into a familiar challenge: real-world flexibility clashes with idealized structures. Simulations can be disrupted by residues adopting unfavored conformations, especially in homology models or modified structures. That’s where interactive editing of dihedral angles becomes essential. The…

When preparing protein structures for molecular dynamics simulations, one common issue is dealing with water molecules in crystal structures. Should you keep them all? Delete them all? The reality is more nuanced, especially when some water molecules are functionally important…

When designing new molecules, one recurring challenge is to understand how small chemical changes affect biological activity or interactions. Whether you’re optimizing binding affinity, reducing toxicity, or simply exploring chemical space, one question often arises: what happens if I slightly…