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Infrared spectroscopy with molecular dynamics
In this exercise, we will compare the vibrational spectrum of two molecules (methanol and benzene) computed with a static method (diagonalization of the dynamical matrix) and with molecular dynamics. The spectra for methanol are available in this paper 10.1039/c3cp44302g. As in the last lectures, to make this exercise computationally feasible, we will use for MD the efficient Density Functional based Tight Binding (DFTB) method. It requires only a minimal basis but delivers nevertheless reasonable results due to an empirical correction term called repulsion potential.
bsub -n 16
, particularly the vibrational spectrum.
Download, as usual, the commented files from the wiki exercise-10.1.tar.gz.
Please use command tar xvf exercise-10.1.tar.gz to extract files.
1. Task: Computing vibrational spectra for methanol and benzene
To compute the vibrational spectra, we first need to find a minimum energy structure for the systems. Use **bsub -n 2** for MD. Here files optc6h6.xyz and optmet.xyz, present in exercise-10.1.tar.gz, contain minimum energy structures. Geometry **optc6h6.xyz** will be the input for the **vibc6h6.inp** and **optmet.xyz** will be the input for the **vibmet.inp**. The following important section (present in the input files) computes the vibrational spectra. <code> &VIBRATIONAL_ANALYSIS INTENSITIES NPROC_REP 16 DX 0.001 &PRINT &PROGRAM_RUN_INFO ON &END &END &END
For the intensities, the derivative of the dipole along the normal modes is necessary (see lecture). So the moments are computed in the standard non-periodic fashion:
&DFT BASIS_SET_FILE_NAME ./BASIS_MOLOPT POTENTIAL_FILE_NAME ./GTH_POTENTIALS &PRINT &MOMENTS PERIODIC FALSE &END &END
This code will generate frequencies and intensities of the IR spectrum in the files C6H6-VIBRATIONS.mol and MET-VIBRATIONS.mol . This file can be read by the visualization program molden.
- $ module load courses mmm
- $ mmm-init
- $ molden C6H6-VIBRATIONS.mol
- Use the “normal mode” check in the graphical interface. The spectrum appears.
- Compare the one of methanol with experiments (see paper) and the one of benzene with literature on the internet.
- Which kind of modes will correspond to stretching of CH and CC bonds?
- Try to animate some frequencies, and report the kind of mode corresponding to all peaks.
Additional Files
Download the following file into your project directory:
You can unpack it with the following command:
$ tar -xvzf dftb_params.tgz
2. Task: Computing vibrational spectra using DFTB molecular dynamics
You will find a fortran program in the repository, called dipole_correlation.f90 Compile it (module load gcc; gfortran -o dipole.x dipole_correlation.f90 ). This program computes the correlation function of the (derivative of) the dipole moment and performs the Fourier transform.
Run cp2k with the md*.inp input files (for the two molecules). Note that the dipole moment and derivatives are extracted from simulation and saved in a file dip*traj (check the input). Run first 5000 steps, then edit the file dipole.in and run dipole.x < dipole.in . This will generate the autocorrelation function of the dipole derivative (why?) and its Fourier transform (frequency domain).
- Run 40000 more steps. Check the new results. Discuss what you obtained. Discuss the behavior of the autocorrelation in the time domain.