CP/MM Tutorial

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vmd -g96 CRD_INI.g96 -cpmd TRAJECTORY 5 – DIPOLE CALCULATION As a last step we want to calculate the dipole moment for each snapshot saved in ten restarts file previously collected and then make the mean value in order to give this way an estimate of the temperature and entropic effects due to the environment formed by the solvent. Create a new folder and copy the restart files and the other needed files in this directory: mkdir DIPOLE_CALCULATION cp ../ PRODUCTION-RUN/RESTART.* . cp ../ PRODUCTION-RUN/gromos* . cp ../ PRODUCTION-RUN/cpmd.inp dipole.in cp ../PRODUCTION-RUN/LATEST . and modify the input file to calculate the dipole moment as you have learnt in the second paragraph: … &CPMD QMMM RESTART WAVEFUNCTION COORDINATES LATEST PROPERTIES RESTFILE 0 &END &PROP DIPOLE MOMENT &END … The keyword LATEST is inserted in order to perform the ten calculations in a comfortable way: in fact, if you want CPMD read the RESTART.X file you only need to replace that name in the first line of the file LATEST. The keyword RESTFILE with value 0 guarantees that CPMD does not write a RESTART file at the end of each calculation (we do not need it, now), so avoiding it overwrites the ones we have copied from the PRODUCTION-‐RUN folder. So, you can perform the following sequence of very fast calculations (less than 3 sec!), being careful to modify the name in the first line of the file LATEST each time:
mpirun -np 2 cpmd.x dipole.inp /home/ei250498/PROGRAMS/SRC/cpmd/PP > dipole1.out & mpirun -np 2 cpmd.x dipole.inp /home/ei250498/PROGRAMS/SRC/cpmd/PP > dipole2.out & mpirun -np 2 cpmd.x dipole.inp /home/ei250498/PROGRAMS/SRC/cpmd/PP > dipole3.out & mpirun -np 2 cpmd.x dipole.inp /home/ei250498/PROGRAMS/SRC/cpmd/PP > dipole4.out & mpirun -np 2 cpmd.x dipole.inp /home/ei250498/PROGRAMS/SRC/cpmd/PP > dipole5.out & mpirun -np 2 cpmd.x dipole.inp /home/ei250498/PROGRAMS/SRC/cpmd/PP > dipole6.out & mpirun -np 2 cpmd.x dipole.inp /home/ei250498/PROGRAMS/SRC/cpmd/PP > dipole7.out & mpirun -np 2 cpmd.x dipole.inp /home/ei250498/PROGRAMS/SRC/cpmd/PP > dipole8.out & mpirun -np 2 cpmd.x dipole.inp /home/ei250498/PROGRAMS/SRC/cpmd/PP > dipole9.out & mpirun -np 2 cpmd.x dipole.inp /home/ei250498/PROGRAMS/SRC/cpmd/PP > dipole10.out & Note: you could have skipped this procedure by using the keyword DIPOLE DYNAMICS SAMPLE 1000 in the previous CP calculation. Such a keyword makes CPMD save the coordinates of the dipole moments every 1000 steps on a file called DIPOLE. An example is saved in the folder: /home/ei250498/TUTORIALS/ACETONE/9-CPMD-MM/4-PRODUCTION-RUN/DIPOLE/ However, these values are polarizations (in a.u.): they have to be multiply by the volume to obtain the correct values of the dipole in a.u. At this point you have only to extract each value of the dipole moment: grep -B 1 -A 4 "X grep -B 1 -A 4 "X Y" dipole1.out Y" dipole2.out … and calculate the arithmetic mean D. What is the difference with respect the value in vacuum we calculate in the second paragraph?
Page 1 and 2: CP/MM Tutorial Jülich, 26/07/2012
Page 3 and 4: Then, you can run molden by simply
Page 5 and 6: we need to write an appropriate inp
Page 7 and 8: The first line gives the number of
Page 9 and 10: NR TYPE X(bohr) Y(bohr) Z(bohr) MBL
Page 11 and 12: NUMBER OF PLANE WAVES FOR WAVEFUNCT
Page 13 and 14: average force on the atoms, and the
Page 15 and 16: RESTART.1 Restart binary file from
Page 17 and 18: g09 opt_geom.com & 3. After about o
Page 19 and 20: edit ACET You can also check if all
Page 21 and 22: Box Density • mkdir analysis •
Page 23 and 24: %FLAG SCEE_SCALE_FACTOR and %FLAG S
Page 25 and 26: simulation is similar to the CPMD i
Page 27 and 28: the according dimension per line. T
Page 29 and 30: TEMPERATURE: EMASS: TIMESTEP: MAXST
Page 31 and 32: MM_CELL_TRANS ENERGIES The QM syste
Page 33 and 34: NOSE ENERGY IONS 0.000000 0.00000 C
Page 35 and 36: cd HEATING • Copy the following f
Page 37: meaningful. Therefore, we must alwa

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