Customizing molecular dynamics (MD) parameters in GROMACS can often feel intimidating, especially for those used to working outside the command line. Researchers might want to experiment with different time steps, thermostats, or barostats, but worry about editing raw .mdp files.…

When preparing membrane protein systems for simulation, one of the most repetitive and time-consuming tasks is building a lipid bilayer around your protein. From aligning the protein to carefully setting up two asymmetric lipid layers, molecular modelers often rely on…

One common challenge in the analysis of molecular simulation results is making sense of how ligands move in and out of protein binding pockets. While numerical data can help quantify these processes, the ability to intuitively visualize the motion of…

When working with molecular models, making consistent changes across multiple atoms, bonds, or residues can be tedious and error-prone. Whether you’re adjusting atom positions, reassigning element types, or updating other attributes, repeating the same modification individually is inefficient. If you’ve…

In molecular modeling, building a lipid bilayer around a membrane protein is often a necessary step for meaningful simulations. Whether you’re preparing a system for molecular dynamics or just visually analyzing structural interplay, constructing a realistic lipid environment can be…

In molecular dynamics setups using GROMACS, defining appropriate index groups is essential when applying center-of-mass (COM) pulling between specific parts of a molecular system. However, this can be a challenge, especially when your regions of interest aren’t part of GROMACS’…

Creating effective molecular presentations is a key part of communicating complex scientific ideas—whether you’re showing binding interactions, illustrating a reaction mechanism, or walking through dynamic conformational changes. However, transitions between animation segments can feel abrupt or visually inconsistent without control…

When refining protein structures, one recurring challenge for modelers is ensuring that all residues adopt conformations that are sterically and energetically reasonable. Outliers in dihedral angles can lead to instability in simulations or incorrect biological interpretations. While tools like structure…

Creating clear and compelling molecular animations can be a challenge—especially when attempting to illustrate large-scale rearrangements, such as ligand binding or the docking of molecular fragments. For many molecular modelers, one of the recurring pains is the tedious manual adjustment…

When modeling molecular transitions between two states, such as during protein-ligand interactions, researchers often rely on the Nudged Elastic Band (NEB) method to compute minimum energy paths. In SAMSON, the integrative molecular design platform, users have two main options to…