. .

Tutorial for the course 'From Molecular to Continuum Physics I'

E. Ippoliti and J. Dreyer


The tutorial provides a short presentation of the procedure to setup a QM/MM calculation by using the CPMD software package and applying it to the simple acetone molecule in water. The second part is on computational spectroscopy including an application of UV/IR spectroscopy of acrolein.


Tutorial material                                                                                                     

 •  QM/MM tutorial
    •  Slides
 •  Browse the QM/MM tutorial files

 •  Thermostats and Barostats

 •  Computational spectroscopy
    •  Exercise: UV spectrum of acrolein		 Acetone in water


Additional material

 •  Jmol:
•  acetone (MD/CPMD)
•  acetone (MOs,Vibrations)
•  formaldehyde (MOs)
•  ethene (MOs,Vibrations)
•  acrolein (Hartree-Fock MOs)
•  acrolein (DFT Orbitals)
•  acrolein (Hartree-Fock Vibrations)
•  acrolein (DFT Vibrations)

 •  Water models
 •  D. Marx, J. Hutter: Ab Initio Molecular Dynamics: Theory and Implementation



Software

 •  VMD
•  VMD 1.8.7 manual
•  VMD tutorial
•  Browse required tutorial files
•  How to visualize CPMD format files 
 •  Gaussian
•  Gaussian 09 manual
 •  CPMD
•  CPMD 3.13.2 manual
•  CPMD: QM/MM section
 •  Amber
•  Amber 11 manual
•  AmberTools 1.4 manual
•  Amber file format
 •  GROMOS
 •  Gromacs
•  Gromacs 4.5.3 manual