How can I calculate the charge distribution of a water molecule?

I would like to obtain the 3D charge density of a water molecule for plotting purposes (i.e. not necessarily super-accurate). I know this is a tough problem, but I'd like to give it a try. Since I'm currently using python, I've identified PyQuante and PySCF, and gather that I should learn how to run density functional theory (DFT) calculations. Before I do that, I'd like to find out if there is something else out there I should use instead. Multiple suggestions are welcome.


I've installed [PyQuante](http://pyquante.sourceforge.net/), which according to it's README.txt may be more accessible to understanding.


For example, the color plots in [this answer](https://chemistry.stackexchange.com/questions/1107/why-is-h%E2%82%82o-a-dipole/1110#1110) give a hint of what I'm talking about, though I'll ultimately plot the field strength contours and some electric field lines.


I'd like to obtain a large table of values (or expressions/expansions?), so I can create and work with surfaces and field line plots myself.


Additionally is it possible that there exist supplementary data in published articles. Where I might find that? Although this is about existing data, I actually do plan on putting in the time to have at least a minimal understanding of the calculation itself. If DFT is it, then I will be spending time studying that.




In [pyscf](https://github.com/sunqm/pyscf), we are routinely running molden.py to generate molden file and plot the orbital surface with Jmol. It should not be too hard to write small script to generate density or other charge surface then plot the surface with Jmol. The basic functions you probably needed should be very close to the functions used by dft module, such as eval\_ao, eval\_rho.


In the recent Pyscf alpha 2 release, a script pyscf/tools/cubegen.py has been added to generate the Gaussian cube file format. In my linux box, the density looks fine in Jmol. You can use it as an example to generate other [Jmol formats](http://wiki.jmol.org/index.php/File_formats/Surfaces).


 7

You need (some) background knowledge and the tools to


* generate an input file with the coordinates of your molecule and commands which calculations to perform
* run the calculation
* postprocess the results


All tools are out there! Unless you have access to the commercially available suites through your institution, I suggest to use those that are free (as in free beer **and** free speech). Actually, some of these free tools are a good choice in any case!


* Input files can be generated using [Avogadro](http://avogadro.cc), [Molden](http://www.cmbi.ru.nl/molden/), [Gabedit](http://gabedit.sourceforge.net/), or [wxmacmolplt](https://code.google.com/p/wxmacmolplt/)
* You can perform your calculations using [NWChem](http://www.nwchem-sw.org/), [MPQC](http://www.mpqc.org/) (both are in the repositories of every recent Linux distribution) or [GAMESS-US](http://www.msg.ameslab.gov/gamess/index.html), which can be downloaded after registration. In addition, there are [pyscf](https://github.com/sunqm/pyscf) and [PyQuante](http://pyquante.sourceforge.net/), which you mentioned in your question.
* Most of the tools used to generate the input files can be used for postprocessing too.


To quote the slogan of a shoe company:



> 
> Just do it!
> 
> 
> 


 6

Two suggestions: [MolCalc](http://molcalc.org/): Calculate Properties > Polarity and Solvation gives you a 3D surface plot with the electrostatic potential superimposed.


Another suggestion is Avogadro/GAMESS/MacMolPlt. See for example [here](http://molecularmodelingbasics.blogspot.dk/2009/11/electron-density.html)


 6

If you are not looking to actually learn these calculations and just need the contour plots, you can use [Arguslab](http://www.arguslab.com/arguslab.com/ArgusLab.html). 


This will give you illustrative plots of orbitals as well as total electron density. They won't be super-accurate but they will be quick.


 5

If you only need the electron density distribution of a water molecule, it doesn't make much sense for you to leanr DFT method. Although I don't think there will be such data out there, it's pretty easy to run such a calculation for people who do DFT calculation regularly. It will take several minutes. My suggestion is that you find someone to help you with the calculation. The calculation could give you the data describing electron density in the 3D space. Then you can play with the data by yourself. 


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