Author: OneAngstrom

Protein-protein docking can be computationally intensive, especially when the search space is left unconstrained. If you know or suspect where a protein binding site lies, one practical way to speed up protein docking is by limiting the search domain. In…

When setting up a coarse-grained (CG) simulation with the MARTINI force field in GROMACS, many modelers run into a subtle but frustrating issue: unrealistic solvent packing that leads to simulation artifacts, often caused by solvent molecules overlapping with the solute…

One of the subtle yet persistent challenges molecular modelers face during molecular dynamics simulations is input file mismanagement—especially during equilibration steps. When performing NVT Equilibration (constant Number of particles, Volume, Temperature), even a small mistake in choosing the right input…

Creating engaging and informative animations is often a challenge in molecular modeling, especially when trying to convey 3D structures and spatial relationships clearly. One recurring issue modelers face is how to make their molecular presentations more dynamic without overwhelming the…

When working on complex molecular modeling projects, collaboration becomes not just helpful, but essential. Whether you’re co-authoring papers, sharing protein structures, or running simulations in the cloud, you need a simple and secure way to manage who sees, edits, or…

When preparing molecular animations, one challenge often faced by researchers and educators is controlling exactly when certain molecules or molecular components become visible in a sequence. Whether you’re highlighting a ligand entering a binding pocket or emphasizing structural reorganization during…

Running molecular simulations in the cloud saves time and computational resources—but comes with its own challenges. How can you monitor your progress, retrieve your data, and fine-tune your workflow without a local copy of everything? That’s where the Job Manager…

When preparing molecular systems for simulations, many researchers overlook a crucial step: neutralizing the system with the proper concentration of ions. This step is simple but can save you hours of troubleshooting down the line when your simulation produces unexpected…