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LAMMPSDataFiles

LAMMPS data file contents vary with respect to your simulation system variables, but all of these files contain two sections: header and properties. This page will look at "atom_style molecular," as this style is used in this group's research.

Header Section

This section relates general information about number of atoms, bonds, dihedrals, impropers and box dimensions. "Parameter types" are also indicated. This feature is primarily used for all-atom simulations. For example in water you have 3 atoms, but 2 different types of atoms (O and H). For a Go-model (which is commonly used in this group) each residue is treated like its own unique "atom" and so these differences are essentially redundant. Also note the first line in the file is ignored during read_data. An example of 1bdd Go-model header:

LAMMPS Description: (First line is ignored)

46 atoms
45 bonds
44 angles
172 dihedrals
0 impropers

46 atom types
45 bond types
44 angle types
172 dihedral types
0 improper types

-791.000000 791.000000 xlo xhi
-791.000000 791.000000 ylo yhi
-791.000000 791.000000 zlo zhi

Properties Section

This section contains individual atom properties and establishes the physics for the system. For "atom_style molecular" we have the necessary sections: Masses, Pair Coeffs, Atoms, Bond Coeffs, Bonds, Angle Coeffs, Angles, Dihedral Coeffs and Dihedrals.
Subsequent sections will have example data with column commentation in (parenthesis). If comments are included in the actual .data file, the simulation will not run.

Masses

This section has two columns, the mass index and the mass(gm/mol).