i want to calculate the charge difference occuring during a chemical reaction. Therefore I have to calculate the charge distribution of the reactants before binding and of the product after the reaction. The idea is to sum up the charge distirbutions of the reactants and subtract it from the charge distribution after reaction. However, therefore it is important to keep the information of the relative position of the fragments with respect to each other. Or with other words, all the calculations must be done on the same grid.
When i calculate the density of the fragments individually it seems that the cube files are moved to the origin. Is there a way to control that qchem does not change the position of the molecules in the plot section.
I already tried to translate the fragements manually after calculating cube files, but it seems that they are not only translated but also slightly rotated, which makes it impossible to reconstruct the initial configuration.
If you have experience in calculating charge difference plots using qchem, please let me know.
The new $plots machinery does translate to the origin but the old machinery uses absolute coordinates. Can you try that? For example,
$plots Plot all four types of quantities 40 -8.0 8.0 40 -8.0 8.0 40 -8.0 8.0 4 3 2 2 28 29 30 31 0 1 2 1 2 1 2 $end
This uses 40 points in each of x,y,z, from -8 to +8 Angst.
Thank you very much!!!
I followed you recommendation, but if I try to write out cube-files I have the same problem again. By addint the keyword IANLTY i get a plot.hf file. This looks fine, but I don’t know how to plot this file-format. Do you have experience with this?
It seems that although I get direct information about the xyz positions of the density values, the molecule is still moved and rotated…
Is any keyword missing? Unfortunately I cannot find any indication in the qchem manual
The plot.hf (for density, and plot.mo for MOs) is some old format that requires post-processing to convert to cube file. It is basically deprecated functionality that I replaced a long time ago with MAKE_CUBE_FILES = TRUE in $rem. When combined with a $plots section, that should return a direction of “filename.cube” files, where “filename” is a reasonably obvious indicator of what’s in each cube file. Please try that approach, which is documented in the manual.