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…

Creating compelling molecular animations can be one of the most time-consuming tasks for researchers preparing publications, presentations, or outreach material. While modern tools offer advanced visualization options, they often lack intuitive ways to manage complex animation timelines, leading to frustration…

Atom selection isn’t always straightforward. If you’re a molecular modeler dealing with large, complex atomic structures, manually selecting atoms that meet specific spatial or chemical criteria can be slow and error-prone. Whether you’re extracting a region of interest or preparing…

One of the common challenges in protein-protein docking is dealing with an overwhelming number of incorrect binding predictions. These false positives can distract from promising candidates and add time-consuming work for researchers manually evaluating results. Fortunately, Hex for SAMSON offers…

When running molecular simulations, a common challenge is the need to experiment interactively with the molecular system — adding or deleting atoms without resetting everything. Whether you’re exploring a reaction mechanism or preparing a structure for refinement, being able to…

If you’re working with complex molecular systems, you’ve probably encountered the challenge of selecting specific subsets of atoms that match your criteria — atoms with certain charges, elements, positions, or structural context. Doing this manually is time-consuming and error-prone, especially…