![]() The fictitios masses distort the forces, shifting some frequencies by as much as few hudreds wavenumbers. Time scale of the simulation is small (just few picosecond). The water molecule is extremely small system, therefore the thermal fluctuations during molecular dynamics are high. One might export spectra into PostScript format or Grace program (on *nix systems) via File menu.ĭue to several reasons, our spectra is quite coarse and noisy. The IR spectra will be plotted by Multiplot plug-in. In order to export spectral data in text format. ![]() You can optionally select Save to File checkbox Multipolt graph of the calculated spectra. The charge of each Wannier center either -2.0 (two electrons) or -1.0 in case of spin polarized calculations.Ĭharge file should be loaded via "Utilities" -> "Load name Charge map from file" menu in the GUI. As we mentioned before, two core 1s electrons represented by pseudopotential. Hence, the value of this charge for oxygen does not correspond to its true atomic charge 8. Where numbers 6.0 and 1.0 represent effective atomic charges of corresponding "pseudoatoms". It will looks like following: # Charges for water molecule + Wannier centers Therefore we have to prepare charge.dat file by ourselves. The guess from CHARMM does not work, because the names Despite of classical molecular dynamics there is no topology file available. In order to get the spectra, charges have to be assigned for all Wannier centers and atoms of interest. We need to supply several parameters from our simulations, namely Time between frames (simulation timestep), Temperature, maximum frequency, type of Correction, etc. Here is the main GUI window of the IR Spec plug-in. Please, note there are only 8 electrons in our system since we use pseudopotentials to describe core electrons.įinally, one can enjoy the dynamics on his own. The other two centers represent bonds between oxygen and hydrogen. The upper two Wannier centers represent two lone pairs of oxygen. The final visualization state water_wannier.vmd file is available. Where Wannier centers represented by transparent green spheres. After proper visualization our water molecule will looks close to the picture on the right. It includes trajectory of the ionis and the Wannier centers On example of the Wannier center dynamics from Car-Parrinello simulation we will calculate IR spectra of water molecule.ĭetails of CPMD simulations are available as a separate tutorial.įirst, we will need IONS+CENTERS.xyz ( 10mb) from that tutorial. The purpose of this tutorial to illustrate the basic capabilities of VMD IRspec plug-in. Water molecule and four wannier centers, corresponding to the two lone pairs and two bonds.
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