For molecular modelers, efficiently exploring the effects of structural modifications on molecular properties can be a challenging task. Whether you’re designing ligands or optimizing bioactivity, pinpointing the optimal molecular analog can feel like searching for a needle in a haystack.…

Molecular modelers often face the challenge of accurately simulating ligand unbinding pathways in protein systems. One significant source of uncertainty in this process is defining an appropriate sampling region, as its size and placement can heavily influence the results. The…

When designing molecular simulations, researchers often encounter the challenge of adequately analyzing specific parts of a molecular system. Standard index groups generated by GROMACS Wizard can sometimes fall short if a study requires tailored selections for detailed exploration. This is…

Prepping a molecular system for coarse-grained simulations can be a daunting task, especially when balancing accuracy with efficiency. If you’ve been struggling to create periodic boxes, solvate systems, and add ions with the right settings, the GROMACS Wizard in SAMSON…

One of the challenges molecular modelers often face when preparing a system for simulations is defining the appropriate periodic box. If the box is too small, your system’s molecules might interact with their periodic images, leading to inaccurate results. On…

For molecular modelers, achieving the desired stability and properties of a molecular system often starts with equilibration. This crucial step ensures that your system reaches realistic temperature, pressure, and density values before commencing full-scale molecular dynamics simulations. But anyone who…

When designing or analyzing molecular structures, precise positioning and alignment are critical tasks that often demand intuitive tools. Whether you’re tweaking atomic placements, aligning meshes, or making large-scale adjustments, efficient movement tools can save you hours of frustration and refine…