Chemistry - Easiest way (software) to visualize charge density from an .xyz file with point-charges?
Solution 1:
After the successful calulation of the electrostatic surface potential, molden equally allows the display of it in a form like
(source)
A step-by-step, hopefully still functional, tutorial is this. (My last contact with Molden already dates back some years.)
Solution 2:
I have found one simple way to do this via Molden:
- Open the .xyz file via Molden:
gmolden myfile.xyz
- Click the "Create Surfaces ...etc." button
- Click Solv. Acc. Surface
- Click Elec. Pot. Mapped
- Click the "Create Surfaces ...etc." button again
- Click Charges Derived
(Optionally, to save the surface, click the "Create Surfaces..." button again and click "Write Surface" and give it a filename.)
I got a visualization like this:
It's not as pretty as I would like, though, so if someone posts an answer with something that looks more like my water example I would be grateful.
Solution 3:
I think this qualifies as a separate answer, using VMD.
I converted the .xyz file to .pdb format (or at least some variant of the strict convention). Thus the file looks like below. The columns are mostly arbitrary, except the coordinates (columns 7,8,9), and charges (column 11).
1) I loaded the file with VMD
2) Clicked (in Main window) Graphics -> Representations
3) Click Coloring Method -> Beta (the column with charges in the .pdb)
4) Click Drawing Method -> QuickSurf
5) Then set these settings: Resolution=0.5, Radius Scale=0.5, Density Isovalue=0.5, Grid Spacing=0.5, and Surface Quality=Max.
6) Clicked (in Main Window) Graphics -> Colors -> Color Scale (tab)
7) Then set these settings: Method=BWR, Offset=-0.03, Midpoint=0.00.
I got this image:
ATOM 1 N MOF F 1 -0.215 -3.612 1.014 14.00700 -0.98043 0.971573 34.722151 3.260689
ATOM 2 N MOF F 1 -0.907 -3.663 -1.269 14.00700 -1.15928 0.971573 34.722151 3.260689
ATOM 3 H MOF F 1 -1.020 -4.516 -1.239 1.00790 0.45173 0.413835 22.141661 2.571134
ATOM 4 H MOF F 1 0.592 -3.533 3.408 1.00790 0.46605 0.413835 22.141661 2.571134
ATOM 5 H MOF F 1 1.138 -4.069 -6.662 1.00790 0.12135 0.413835 22.141661 2.571134
ATOM 6 Zn MOF F 1 1.049 0.362 1.462 65.39000 1.08557 1.988700 62.399227 2.461553
ATOM 7 C MOF F 1 0.826 0.806 4.183 12.01100 0.88512 1.288599 52.838055 3.430851
ATOM 8 C MOF F 1 0.417 1.494 5.456 12.01100 -0.15826 1.288599 52.838055 3.430851
ATOM 9 C MOF F 1 -0.186 2.734 5.458 12.01100 -0.03822 1.288599 52.838055 3.430851
ATOM 10 H MOF F 1 -0.320 3.185 4.658 1.00790 0.11123 0.413835 22.141661 2.571134
ATOM 11 N MOF F 1 3.030 0.215 1.014 14.00700 -0.98970 0.971573 34.722151 3.260689
ATOM 12 N MOF F 1 2.978 0.907 -1.269 14.00700 -1.32379 0.971573 34.722151 3.260689
ATOM 13 H MOF F 1 2.125 1.020 -1.239 1.00790 0.55292 0.413835 22.141661 2.571134
ATOM 14 H MOF F 1 3.108 -0.592 3.408 1.00790 0.59979 0.413835 22.141661 2.571134
ATOM 15 O MOF F 1 0.611 1.412 3.077 15.99980 -0.80546 0.851973 30.193174 3.118146
ATOM 16 O MOF F 1 1.326 -0.316 4.242 15.99980 -0.78673 0.851973 30.193174 3.118146
ATOM 17 C MOF F 1 -0.826 -0.806 -9.142 12.01100 0.93207 1.288599 52.838055 3.430851
ATOM 18 C MOF F 1 -0.417 -1.494 -7.869 12.01100 -0.11669 1.288599 52.838055 3.430851
ATOM 19 C MOF F 1 0.186 -2.734 -7.867 12.01100 -0.09239 1.288599 52.838055 3.430851
ATOM 20 H MOF F 1 0.320 -3.185 -8.666 1.00790 0.11624 0.413835 22.141661 2.571134
ATOM 21 O MOF F 1 -0.611 -1.412 -10.248 15.99980 -0.90874 0.851973 30.193174 3.118146
ATOM 22 O MOF F 1 -1.326 0.316 -9.083 15.99980 -0.83883 0.851973 30.193174 3.118146
ATOM 23 C MOF F 1 -0.487 -3.006 -0.183 12.01100 1.02987 1.288599 52.838055 3.430851
ATOM 24 C MOF F 1 0.218 -2.574 1.792 12.01100 1.08445 1.288599 52.838055 3.430851
ATOM 25 N MOF F 1 -0.287 -1.704 -0.139 14.00700 -0.55634 0.971573 34.722151 3.260689
ATOM 26 N MOF F 1 0.174 -1.421 1.164 14.00700 -0.66953 0.971573 34.722151 3.260689
ATOM 27 H MOF F 1 -1.063 -3.236 -1.999 1.00790 0.47914 0.413835 22.141661 2.571134
ATOM 28 N MOF F 1 0.588 -2.746 3.065 14.00700 -1.21993 0.971573 34.722151 3.260689
ATOM 29 H MOF F 1 0.822 -2.067 3.539 1.00790 0.53567 0.413835 22.141661 2.571134
ATOM 30 Zn MOF F 1 -1.049 -0.362 -1.462 65.39000 1.11531 1.988700 62.399227 2.461553
ATOM 31 C MOF F 1 -0.826 -0.806 -4.183 12.01100 0.93024 1.288599 52.838055 3.430851
ATOM 32 C MOF F 1 -0.417 -1.494 -5.456 12.01100 -0.16513 1.288599 52.838055 3.430851
ATOM 33 C MOF F 1 0.186 -2.734 -5.458 12.01100 -0.06813 1.288599 52.838055 3.430851
ATOM 34 H MOF F 1 0.320 -3.185 -4.658 1.00790 0.12591 0.413835 22.141661 2.571134
ATOM 35 C MOF F 1 -3.635 -0.487 0.183 12.01100 1.11280 1.288599 52.838055 3.430851
ATOM 36 C MOF F 1 -4.067 0.218 -1.792 12.01100 1.08992 1.288599 52.838055 3.430851
ATOM 37 N MOF F 1 -4.937 -0.287 0.139 14.00700 -0.66901 0.971573 34.722151 3.260689
ATOM 38 N MOF F 1 -5.220 0.174 -1.164 14.00700 -0.68365 0.971573 34.722151 3.260689
ATOM 39 N MOF F 1 -3.030 -0.215 -1.014 14.00700 -1.01056 0.971573 34.722151 3.260689
ATOM 40 N MOF F 1 -2.978 -0.907 1.269 14.00700 -1.37928 0.971573 34.722151 3.260689
ATOM 41 H MOF F 1 -3.406 -1.063 1.999 1.00790 0.46532 0.413835 22.141661 2.571134
ATOM 42 H MOF F 1 -2.125 -1.020 1.239 1.00790 0.59146 0.413835 22.141661 2.571134
ATOM 43 N MOF F 1 -3.896 0.588 -3.065 14.00700 -1.35982 0.971573 34.722151 3.260689
ATOM 44 H MOF F 1 -4.575 0.822 -3.539 1.00790 0.46237 0.413835 22.141661 2.571134
ATOM 45 H MOF F 1 -3.108 0.592 -3.408 1.00790 0.59502 0.413835 22.141661 2.571134
ATOM 46 O MOF F 1 -0.611 -1.412 -3.077 15.99980 -0.84629 0.851973 30.193174 3.118146
ATOM 47 O MOF F 1 -1.326 0.316 -4.242 15.99980 -0.78990 0.851973 30.193174 3.118146
ATOM 48 C MOF F 1 0.487 3.006 0.183 12.01100 1.05481 1.288599 52.838055 3.430851
ATOM 49 C MOF F 1 -0.218 2.574 -1.792 12.01100 1.07969 1.288599 52.838055 3.430851
ATOM 50 N MOF F 1 0.287 1.704 0.139 14.00700 -0.59652 0.971573 34.722151 3.260689
ATOM 51 N MOF F 1 -0.174 1.421 -1.164 14.00700 -0.65162 0.971573 34.722151 3.260689
ATOM 52 N MOF F 1 0.215 3.612 -1.014 14.00700 -0.98211 0.971573 34.722151 3.260689
ATOM 53 N MOF F 1 0.907 3.663 1.269 14.00700 -1.15390 0.971573 34.722151 3.260689
ATOM 54 H MOF F 1 1.063 3.236 1.999 1.00790 0.47225 0.413835 22.141661 2.571134
ATOM 55 H MOF F 1 1.020 4.516 1.239 1.00790 0.44830 0.413835 22.141661 2.571134
ATOM 56 N MOF F 1 -0.588 2.746 -3.065 14.00700 -1.19279 0.971573 34.722151 3.260689
ATOM 57 H MOF F 1 -0.822 2.067 -3.539 1.00790 0.51149 0.413835 22.141661 2.571134
ATOM 58 H MOF F 1 -0.592 3.533 -3.408 1.00790 0.45861 0.413835 22.141661 2.571134
ATOM 59 C MOF F 1 0.599 -3.311 -6.662 12.01100 -0.25368 1.288599 52.838055 3.430851
ATOM 60 C MOF F 1 -0.739 -0.894 -6.662 12.01100 -0.06065 1.288599 52.838055 3.430851
ATOM 61 H MOF F 1 -1.177 -0.074 -6.662 1.00790 0.13569 0.413835 22.141661 2.571134
ATOM 62 C MOF F 1 0.826 0.806 9.142 12.01100 0.92157 1.288599 52.838055 3.430851
ATOM 63 C MOF F 1 0.417 1.494 7.869 12.01100 -0.13626 1.288599 52.838055 3.430851
ATOM 64 C MOF F 1 -0.186 2.734 7.867 12.01100 -0.03347 1.288599 52.838055 3.430851
ATOM 65 H MOF F 1 -0.320 3.185 8.666 1.00790 0.09270 0.413835 22.141661 2.571134
ATOM 66 O MOF F 1 0.611 1.412 10.248 15.99980 -0.90075 0.851973 30.193174 3.118146
ATOM 67 O MOF F 1 1.326 -0.316 9.083 15.99980 -0.83647 0.851973 30.193174 3.118146
ATOM 68 C MOF F 1 -0.599 3.311 6.662 12.01100 -0.29931 1.288599 52.838055 3.430851
ATOM 69 H MOF F 1 -1.138 4.069 6.662 1.00790 0.13426 0.413835 22.141661 2.571134
ATOM 70 C MOF F 1 0.739 0.894 6.662 12.01100 -0.04864 1.288599 52.838055 3.430851
ATOM 71 H MOF F 1 1.177 0.074 6.662 1.00790 0.13042 0.413835 22.141661 2.571134
ATOM 72 C MOF F 1 3.635 0.487 -0.183 12.01100 1.07120 1.288599 52.838055 3.430851
ATOM 73 C MOF F 1 4.067 -0.218 1.792 12.01100 1.08532 1.288599 52.838055 3.430851
ATOM 74 N MOF F 1 4.937 0.287 -0.139 14.00700 -0.66095 0.971573 34.722151 3.260689
ATOM 75 N MOF F 1 5.220 -0.174 1.164 14.00700 -0.67297 0.971573 34.722151 3.260689
ATOM 76 H MOF F 1 3.406 1.063 -1.999 1.00790 0.45974 0.413835 22.141661 2.571134
ATOM 77 N MOF F 1 3.896 -0.588 3.065 14.00700 -1.35657 0.971573 34.722151 3.260689
ATOM 78 H MOF F 1 4.575 -0.822 3.539 1.00790 0.45717 0.413835 22.141661 2.571134
Solution 4:
I think, the easiest way is to use Multiwfn in combination with Jmol. There you can estimate/rebuild the ESP from partial charges.
Multiwfn
Load your xyz file with the charges into Multiwfn, which should recognize the charges. If not, then remove the first two lines and rename it into file.chg
.
5 Output and plot specific property within a spatial region (calc. grid data)
8 Electrostatic potential from nuclear charges
3 High quality grid , covering whole system, about 1728000 points in total
2 Export data to Gaussian cube file in current folder
Now you should have a file called nucleiesp.cub
, which is a Gaussian cube file.
Next thing that you need is a cube file, that contains the electron density. That should be possible to obtain with NWChem. If not, then somehow get a molden file and build the cube file also in Multiwfn using 5 > 1 > 3 > 2
.
Jmol
In Jmol you make a right click in the black area and choose the console. There you simply write: load "path/to/files/geom.xyz"; isosurface myiso cutoff 0.002 "path/to/files/density.cub" map "path/to/files/nucleiesp.cub"; show $myiso; color $myiso "rwb"; color $myiso translucent
and you will get an image like this:
This is the red-white-blue-colored translucent ESP on the electron density (isovalue 0.002).
If you don’t have the option to get the density, you can also use the SAS, the surface accessible surface, which would then look like this:
load "D:/calculations/mwfn-charges2esp/geom.xyz"; isosurface myiso solvent map "D:/calculations/mwfn-charges2esp/nucleiesp.cub"; show $myiso; color $myiso "rwb"; color $myiso translucent
PovRay
One way to get nice pictures out of Jmol is to render them with PoyRay, but as I am no expert with Jmol, I am a far less expert with PovRay. So the result is only kind of a "preview" on what you get without any effort.
Because I didn’t like the big atoms, I changed the atom size resp. the sphere radius macro in the Jmol.pov file like following:
#macro a(X,Y,Z,RADIUS,R,G,B,T)
sphere{<X,Y,Z>,RADIUS/5
pigment{rgbt<R,G,B,T>}
translucentFinish(T)
clip()
check_shadow()}
#end
which ends up in an image like this: