DeCipher - Theory. 2 Theory Molecular properties DeCipher's philosophy revolves around mathematical and geometrical modeling of molecular properties. In DeCipher, there are two broad categories of molecular properties. Basic molecular properties are represented as simple mathematical functions of atomic variables directly accessible from molecular structure databases or molecular simulations trajectory files: atom coordinates, velocities, charges, masses, etc. These basic properties are referred to as "Functions" in the program. Once they are defined basic properties can be visualized, measured, monitored, and correlated over time. High level properties are also functions, in the mathematical sense, of atomic variables and time (i.e., configurations). For more information on atomic attributes, refer to the Molecular subsets heading in Chapter 3, Languages. Nomenclature In the following, we will use the word "particle" to refer to either an atom, a residue, a molecule, or an arbitrary set of atoms.
Eq. 1 Eq. 2. Water models. Documentation. Home MD. Mathematica Packages. Packmol - Starting Configurations for Molecular Dynamics Through Packing. Mdanalysis - A python library to analyze and manipulate molecular dynamics trajectories.