PDB (Protein Data Bank)

The VASP (Vienna Ab initio Simulation Package) is a widely used software package for quantum mechanical molecular dynamics simulations. In VASP, the information about the structure, including atomic positions and unit cell parameters, is typically specified in the POSCAR file. Below is an example of a simplified POSCAR file for a water molecule:

Water Molecule
1.0
   5.0  0.0  0.0
   0.0  5.0  0.0
   0.0  0.0  5.0
O   H
3   3
Direct
 0.00000  0.00000  0.00000
 0.75700  0.58600  0.00000
-0.75700  0.58600  0.00000

In this example:

  • The first line indicates a comment.

  • The second line is a scaling factor for the lattice vectors (here, set to 1.0).

  • The next three lines define the lattice vectors of the unit cell.

  • The following line specifies the chemical elements present in the structure (in this case, oxygen (O) and hydrogen (H)).

  • The next line indicates the number of atoms of each type.

  • The line with “Direct” denotes that the atomic coordinates are given in fractional coordinates.

  • The subsequent lines provide the fractional coordinates of each atom.

This POSCAR file represents a water molecule with a cubic unit cell. The actual structure and unit cell

parameters should be adjusted based on the specific system you are studying. Always consult the VASP documentation for accurate and up-to-date information on the POSCAR file format and parameters.