Files generated by the interface code

• QMMM_ORDER
  The first line specifies the total number of atoms (NAT) and the number of quantum atoms (NATQ). The subsequent NAT lines contain, for every atom, the gromos atom number, the internal CPMD atom number, the CP species number isp and the number in the list of atoms for this species NA(isp). The quantum atoms are specified in the first NATQ lines.

• CRD_INI.grm
  Contains the positions of all atoms in the first frame of the simulation in Gromos extended format (g96).

• CRD_FIN.grm
  Contains the positions of all atoms in the last frame of the simulation in Gromos extended format (g96).

• INTERACTING.pdb
  Contains (in a non-standard PDB-like format) all the QM atoms and all the MM atoms in the electrostatic coupling NN list. The 5-th column in this file specifies the gromos atom number as defined in the topology file and in the coordinates file. The 10-th column specifies the CPMD atom number as in the TRAJECTORY file. The quantum atoms are labeled by the residue name QUA.

• INTERACTING_NEW.pdb
  The same as INTERACTING.pdb, but it is created if the file INTERACTING.pdb is detected in the current working directory of the CPMD run.

• TRAJECTORY_INTERACTING
  Contains the coordinates and the velocities (in TRAJECTORY format) of the atoms listed in INTERACTING.pdb. The format is the same as in the files TRAJECTORY and MOVIE, hence frames belonging to different runs are separated by the line ««< NEW DATA »»>.

  The atoms in this file do not necessarily coincide with the NN atoms, that are written at every update of the pair list in the file INTERACTING_NEW.pdb.

• MOVIE_INTERACTING
  The MOVIE-like file corresponding to TRAJECTORY_INTERACTING.

• ESP
  Contains the ESP charges of the QM atoms in CPMD order (the corresponding Gromos numbers can be found in QMMM_ORDER). The first column is the frame number.

• EL_ENERGY
  Contains the electrostatic interaction energy. First column: frame number. Second column: total electrostatic interaction energy. Other columns: interaction energy of the NN atoms with the QM system; interaction energy with the ESP coupled atoms; multipolar interaction energy; electrostatic interaction energy evaluated using the classical force field charges for the QM atoms.

• MULTIPOLE
  Contains, for every frame (specified in the first column), the three components of the dipol D(ix) and the five independent components of the quadrupole Q(ix,jx) of the quantum system in a.u. The order is: D(1),D(2),D(3),Q(1,1),Q(2,2),Q(1,2),Q(1,3),Q(2,3).

• MM_CELL_TRANS
  Contains, the Trajectory of the re-centering offset for the QM-box. The first column ist the frame number (NFI) followed by the x-, y-, and z-component of the cell-shift vector.