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Atomic Coordinates

The coordinates file fed to the coordinates parameter should be either in XMol (also called "xyz") or PDB format. In an XMol coordinates file, the first line specifies the number of atoms, and the second line provides a description of the system (it can be left blank). Atomic coordinates are listed starting from the third line. All coordinates are either in Angstroms (default) or Bohrs (this can be specified in the start file). Here is an example coordinates file for a hydrogen molecule:

h2.xyz
2
Hydrogen Molecule -- Xmol format
H 0.0 0.0 0.0
H 0.7 0.0 0.0

Some jobs (for example, transition state search using NEB method) require several sets of coordinates (frames). In this case all frames should be listed in the coordinates file one by one, i.e.

h2-2frames.xyz
2
Hydrogen Molecule -- Xmol format frame 1
H 0.0 0.0 0.0
H 0.7 0.0 0.0
2
Hydrogen Molecule -- Xmol format frame 2
H 0.0 0.0 0.0
H 0.8 0.0 0.0

Note There should be no blank lines between individual frames.

The PDB format often used for protein molecules is also supported and will be automatically assumed if the filename for the coordinates ends in ‘.pdb’. More details on PDB file format are available at http://www.wwpdb.org/docs.html

Ghost atoms

Sometimes it is useful to include the basis functions of an atom without including its nucleus or electrons. The canonical application is the Boys-Bernardi counterpoise correction for basis-set superposition error (BSSE),1 in which the interaction energy of two fragments is computed as

\[E^{\text{cp}}_{AB} = E_{AB}(R_A, R_B; A \cup B) - E_A(R_A; A \cup B) - E_B(R_B; A \cup B),\]

where the second argument inside each parenthesis is the basis set used. In the second and third terms, only the atoms of one fragment are present, but the basis functions of both fragments are used. The "extra" basis-function sites on the missing fragment are the ghost atoms.

In TeraChem, ghost atoms are flagged in the coordinate file by prefixing the element symbol with the letter X. For example, this coordinate file puts a real water molecule at the top and three ghost atoms (the basis functions of a second water) at the bottom:

water_dimer_with_ghosts.xyz
6

O   -0.029481  -0.086991  -0.533710
H   -0.660044  -0.772698  -0.712077
H    0.086741   0.049151   0.406478
XO   0.306708   0.307377   2.262155
XH   1.109626   0.019913   2.679671
XH  -0.049150   1.088298   2.668550

This system has only 10 electrons (one O nucleus and two H nuclei in the real fragment), but basis functions are placed on all six listed positions according to the basis set selected in the input file. Repeating the calculation with the roles of real and ghost atoms swapped, plus a third calculation with both fragments real, gives the three energies needed for the counterpoise correction above.

  1. S. F. Boys and F. Bernardi, Mol. Phys. 19, 552-566 (1970). ↩