For example, if you use the or modules, please cite:ĭouglas L. MDAnalysis includes many algorithms and modules that should also be individually cited. Rostrup, editors, Proceedings of the 15th Python in Science Conference, pages 98-105, Austin, TX, 2016. MDAnalysis: A Python package for the rapid analysis of molecular dynamics simulations. MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations. When using MDAnalysis in published work, please cite both these papers: For example, an AtomGroup used to create a bond can only have 2 atoms in it an AtomGroup used to create a dihedral or improper angle must have 4 atoms. This AtomGroup has a special requirement: only the atoms involved in the geometry can be in the group. MDAnalysis can also create topology geometries such as bonds, angles, dihedral angles, and improper angles from an AtomGroup. To be certain that MDAnalysis is using the correct masses, you can set them manually. If MDAnalysis has no idea what the particle is (e.g. coarse-grained beads), it will raise a warning, and give that particle a mass of 0. If MDAnalysis guesses incorrectly (e.g. a calcium atom called CA is treated as a \(C_\)), the mass of that atom will be inaccurate. Particle masses may not always be available or accurate!Ĭurrently, MDAnalysis assigns masses to particles based on their element or ‘atom type’, which is guessed from the particle name. center_of_mass() function, like many of the analysis modules in MDAnalysis, relies on having accurate mass properties available. This structure is important because it allows MDAnalysis to work with trajectory files too large to fit into the computer’s memory. Think of the trajectory as a function \(X(t)\) of the frame index \(t\) that only makes the data from this specific frame available. The trajectory attribute of a Universe is usually a file reader. trajectory.Ī fundamental concept in MDAnalysis is that at any one time, only one time frame of the trajectory is being accessed. atoms attribute, and combines it with a trajectory at. See Working with atoms below.Ī Universe contains all the particles in a molecular system in an AtomGroup accessible at the. The AtomGroup is probably the most important class in MDAnalysis, as almost everything can be accessed through it. A particle is represented as an Atom object, even if it is a coarse-grained bead.Ītoms are grouped into AtomGroups. Several key data structures form the backbone of MDAnalysis.Ī molecular system consists of particles. MDAnalysis is a Python package that provides tools to access and analyse data in molecular dynamics trajectories. Standard residues in MDAnalysis selections.Getting atom information from AtomGroups.