One of the challenges molecular modelers often face is identifying physically meaningful transition paths between molecular conformations. If you’ve ever struggled with refining a rough transition path, the Parallel Nudged Elastic Band (P-NEB) app in SAMSON offers an efficient and…

Molecular modelers often face the challenge of effectively visualizing dynamic processes like trajectories or transitions between conformations. These dynamic visualizations can be crucial for understanding molecular mechanisms and communicating findings. To help address this, SAMSON provides a simple yet powerful…

For molecular modelers working on detailed animations, maintaining a consistent camera perspective can be a common challenge. As you modify your model, interact with the system, or cycle through animations, the camera view can unintentionally drift, disrupting your work. Thankfully,…

If you are involved in molecular modeling or structural biology, understanding protein dynamics is key to your work. One critical motion that has captured global scientific attention is the opening and closing of the SARS-CoV-2 spike protein. This motion is…

For molecular modelers, one common challenge is efficiently examining and analyzing the results of production molecular dynamics simulations. With large-scale data and multiple output files, understanding what to extract and how to extract it can be daunting. The GROMACS Wizard…

For molecular modelers working with GROMACS, defining index groups is often critical for applying advanced workflows like pulling motions, isolating subsets of residues, or preparing for analysis. While the default GROMACS index groups are sufficient for standard tasks, there are…

Capturing a precise molecular view and keeping it unchanged during animations or presentations is a common challenge for molecular modelers. Whether you’re showcasing molecular interactions or presenting a highly detailed zoom, the Hold camera animation in SAMSON offers a straightforward…