Mastering Custom Index Groups for GROMACS Simulations

One of the common challenges faced by molecular modelers working with GROMACS is effectively organizing and analyzing systems with complex molecular compositions. Whether it’s assigning atoms for pulling simulations, defining analysis regions, or creating specialized workflows, the ability to include…

Streamline Molecular Animations with Path Recording in SAMSON.

For molecular modelers, showcasing molecular trajectories and ensuring a seamless presentation of dynamic processes can often be a logistical headache. Whether you’re visualizing ligand docking, simulating atomic movements, or assembling molecular structures, it’s crucial to accurately capture and export these…

Better Molecular Models: Exploring Symmetry Mates in Proteins

Understanding protein structures and their interactions is a fundamental task for molecular modelers. Yet, reconstructing biologically meaningful assemblies from raw structural data can sometimes feel like piecing together a puzzle with missing edges. This is where SAMSON’s Symmetry Mate Editor…

Streamline Molecular Workflows with Python in SAMSON.

Molecular modeling often involves repetitive and complex workflows that are ideal candidates for automation. If you’ve ever wished for a way to save time and boost the reproducibility of your computational experiments, Python scripting within SAMSON presents a compelling solution.…

Simplify Molecular Simulations with SAMSON’s Setup Workflows

Molecular modeling is often a meticulous process requiring careful setup for simulations. Between preparing your biomolecular system, choosing the correct force field, and addressing warnings, this step can become a bottleneck. Fortunately, SAMSON’s integrative molecular design platform offers structured workflows…

How to Use a Custom GROMACS Version in GROMACS Wizard

Molecular modelers often face challenges when trying to ensure reproducibility or optimize their computational setup for molecular dynamics simulations. One recurring challenge is the need to use a specific version of GROMACS, particularly when the packaged version does not meet…