CP/MM Tutorial

• Finally remember that under the CELL keyword of the CPMD input file the
size of the quantum cell will be inserted according to the syntax:
size_x size_y/size_x size_z/size_x 0 0 0
1 - ANNEALING
We are now ready to run the annealing (copy all the file in a folder called
ANNEALING):
mpirun -np 2 cpmd.x annealing.inp /home/ei250498/PROGRAMS/SRC/cpmd/PP
> annealing.out &
While the simulation proceeds you can monitor the decreasing temperature (third
column named TEMPP) this way:
tail -f annealing.out
When the temperature reaches about 2-4 K we can “softly” stop the calculation (that
is in order to make it write a RESTART file) by typing on the prompt line:
touch EXIT
The final configuration will be stored in the RESTART.1 file.
More files will be generated during a QM/MM CP simulation:
QMMM_ORDER
CRD_INI.g96
CRD_FIN.g96
INTERACTING.pdb
INTERACTING_NEW.pdb
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.
Contains the positions of all atoms in the first frame of the
simulation in Gromos extended format (g96).
Contains the positions of all atoms in the last frame of the
simulation in Gromos extended format (g96).
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.
The same as before, but it is created if the file
INTERACTING.pdb is detected in the current working
directory of the CPMD run.