Easiest way (software) to visualize charge density from an .xyz file with point-charges?

Question

I have an .xyz file which contains partial charges calculated by a Quantum-Chemistry software (NWChem).

The system looks like this, here I show the partial charges calculated from the electrostatic surface potential (using CHELPG method).

I want something like this classic example of water (red is showing high electron density while blue shows low), e.g. to demonstrate polarity and electronic structure:

Is it possible to get this from point-charge data (as opposed to a very large set of points)? I'm familiar with VMD, Avogadro, and other visualization softwares but I don't know a way off-hand to accomplish this. Here is the .xyz file itself (charges are the 5th column):

78

 N  -0.215180  -3.611590   1.013730  -0.980426
 N  -0.907220  -3.663400  -1.269030  -1.159281
 H  -1.020120  -4.516150  -1.239180   0.451727
 H   0.592410  -3.533220   3.408420   0.466050
 H   1.138340  -4.068520  -6.662270   0.121348
Zn   1.048810   0.361560   1.461840   1.085568
 C   0.826190   0.806270   4.182580   0.885122
 C   0.417080   1.494320   5.455600  -0.158259
 C  -0.185960   2.733600   5.457730  -0.038223
 H  -0.320120   3.185220   4.658260   0.111225
 N   3.029810   0.215180   1.013730  -0.989702
 N   2.978000   0.907220  -1.269030  -1.323792
 H   2.125250   1.020120  -1.239180   0.552920
 H   3.108180  -0.592410   3.408420   0.599787
 O   0.611010   1.411960   3.076910  -0.805465
 O   1.325620  -0.316130   4.242000  -0.786727
 C  -0.826190  -0.806270  -9.141970   0.932072
 C  -0.417080  -1.494310  -7.868950  -0.116686
 C   0.185960  -2.733600  -7.866810  -0.092391
 H   0.320120  -3.185210  -8.666290   0.116237
 O  -0.611010  -1.411960 -10.247640  -0.908737
 O  -1.325620   0.316130  -9.082550  -0.838830
 C  -0.487480  -3.005900  -0.183350   1.029873
 C   0.217840  -2.574210   1.791620   1.084450
 N  -0.286910  -1.704180  -0.139370  -0.556339
 N   0.174010  -1.421260   1.164300  -0.669532
 H  -1.062620  -3.235690  -1.998680   0.479136
 N   0.588430  -2.745550   3.064650  -1.219932
 H   0.822210  -2.066800   3.539000   0.535669
Zn  -1.048810  -0.361560  -1.461840   1.115312
 C  -0.826190  -0.806270  -4.182580   0.930235
 C  -0.417080  -1.494310  -5.455600  -0.165126
 C   0.185960  -2.733600  -5.457740  -0.068129
 H   0.320120  -3.185210  -4.658260   0.125910
 C  -3.635500  -0.487480   0.183350   1.112801
 C  -4.067190   0.217840  -1.791620   1.089920
 N  -4.937220  -0.286910   0.139380  -0.669012
 N  -5.220140   0.174010  -1.164300  -0.683650
 N  -3.029810  -0.215180  -1.013730  -1.010564
 N  -2.978000  -0.907210   1.269030  -1.379275
 H  -3.405710  -1.062620   1.998680   0.465316
 H  -2.125250  -1.020120   1.239180   0.591458
 N  -3.895840   0.588430  -3.064650  -1.359821
 H  -4.574600   0.822210  -3.539000   0.462374
 H  -3.108170   0.592410  -3.408420   0.595021
 O  -0.611010  -1.411960  -3.076900  -0.846291
 O  -1.325620   0.316130  -4.242000  -0.789904
 C   0.487480   3.005900   0.183350   1.054807
 C  -0.217840   2.574210  -1.791620   1.079690
 N   0.286910   1.704180   0.139380  -0.596520
 N  -0.174000   1.421260  -1.164300  -0.651619
 N   0.215180   3.611590  -1.013730  -0.982105
 N   0.907220   3.663400   1.269030  -1.153898
 H   1.062620   3.235690   1.998680   0.472248
 H   1.020120   4.516150   1.239180   0.448303
 N  -0.588430   2.745550  -3.064650  -1.192789
 H  -0.822210   2.066800  -3.539000   0.511494
 H  -0.592410   3.533220  -3.408420   0.458606
 C   0.599050  -3.311400  -6.662270  -0.253677
 C  -0.738520  -0.893930  -6.662270  -0.060650
 H  -1.176860  -0.074380  -6.662270   0.135692
 C   0.826190   0.806270   9.141970   0.921571
 C   0.417080   1.494320   7.868950  -0.136263
 C  -0.185960   2.733600   7.866820  -0.033469
 H  -0.320120   3.185220   8.666290   0.092701
 O   0.611010   1.411960  10.247650  -0.900753
 O   1.325620  -0.316130   9.082550  -0.836472
 C  -0.599050   3.311400   6.662270  -0.299314
 H  -1.138340   4.068520   6.662270   0.134260
 C   0.738520   0.893930   6.662270  -0.048643
 H   1.176860   0.074380   6.662270   0.130420
 C   3.635500   0.487480  -0.183350   1.071205
 C   4.067190  -0.217840   1.791620   1.085316
 N   4.937220   0.286910  -0.139370  -0.660949
 N   5.220140  -0.174000   1.164300  -0.672967
 H   3.405710   1.062620  -1.998680   0.459743
 N   3.895850  -0.588430   3.064650  -1.356568
 H   4.574600  -0.822210   3.539000   0.457166

Buttonwood · Accepted Answer · 2017-06-21 22:23:37Z

9

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.)

edited Jun 21, 2017 at 22:23

answered Jun 21, 2017 at 22:20

Buttonwood

28.4k2 gold badges43 silver badges102 bronze badges

$\begingroup$ Using Molden to calculate the charges is undesirable / unpreferred in my case. I've seen this tutorial before, and it was helpful, but I was looking for a way to get the surface straight from an .xyz with point-charges. I discovered ways to do that in my answers. Thanks again! $\endgroup$
– khaverim
Jun 22, 2017 at 21:30

Add a comment |

pH13 - Yet another Philipp · Accepted Answer · 2017-06-24 18:23:05Z

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:

I just saw, that in my last image the hydrogens are a little too small. So using RADIUS/2 makes the PoyRay atom size look like in Jmol. — pH13 - Yet another Philipp, Jun 25, 2017 at 14:13

khaverim · Accepted Answer · 2017-06-21 22:51:49Z

8

I have found one simple way to do this via Molden:

Open the .xyz file via Molden: gmolden myfile.xyz
1. Click the "Create Surfaces ...etc." button
2. Click Solv. Acc. Surface
3. Click Elec. Pot. Mapped
4. Click the "Create Surfaces ...etc." button again
5. 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.

answered Jun 21, 2017 at 22:51

khaverim

3,56417 silver badges33 bronze badges

1

$\begingroup$ I think molden can export the result as a cube file which you can probably visualize afterwards with Avogadro. $\endgroup$
– pH13 - Yet another Philipp
Jun 24, 2017 at 18:36

Add a comment |

khaverim · Accepted Answer · 2017-06-22 16:59:47Z

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

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Easiest way (software) to visualize charge density from an .xyz file with point-charges?

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