Molecular modeling and simulation often involve handling large trajectory files produced by molecular dynamics engines like GROMACS, AMBER, NAMD, LAMMPS, and Tinker. However, switching between simulation and visualization tools can feel like constantly battling with incompatible data formats and slow…
Many researchers and developers in molecular modeling rely on custom scripts, external executables, or web services to perform specific tasks—such as docking, calculations, or data analysis. However, managing multiple tools can be time-consuming, especially when interoperability isn’t seamless. This is…
When modeling molecular transitions such as ligand unbinding or conformational changes in biomolecules, predicting realistic pathways is often critical, but far from straightforward. Finding the most efficient and accurate approach can save time and computing resources, especially when working with…
When working with protein structures, accuracy begins at preparation. One common issue molecular modelers face—especially when dealing with alternate conformations or large multimeric structures—is the need to remove unwanted chains before running simulations, conformational interpolation, or structural comparisons. For instance,…
Capturing molecular flexibility is an essential part of modern structural biology and computational modeling. Whether you’re exploring ligand accessibility, visualizing allosteric motions, or preparing morphing animations between conformations, there often comes a time when you reach an interesting molecular state…
