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After I have done with some Monte Carlo simulation of Gay-Berne model, I want to visualize how the N molecules look like in the domain. Here the N molecules all have the same ellipsoidal shape. The centre positions $\mathbf{r}_i$ and the orientations $\mathbf{u}_i$ are given. Is there any software that can plot the configuration of these N molecules based on the given information? Either 3D or 2D is fine.


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Almost any mathematical package will suffice: Matlab, Mathematica, Sage, ... Here is an image made in Mathematica, with the ellipses drawn by the Circle[] function, and then oriented with Rotate[]:
One can also draw 3D ellipsoids in these packages. See the earlier MO question, "Maximual tetrahedra inscribed in an ellipsoid" for an example (using Rotate[Scale[Sphere[]]]).

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I found that pdeellip() in Matlab has similar functionality. Thanks a lot! –  Chong Luo Oct 25 '11 at 11:50
Yes. Here is the man page on that Matlab function, in case anyone wants to use it: mathworks.com/help/toolbox/pde/ug/pdeellip.html –  Joseph O'Rourke Oct 25 '11 at 12:11
For N=1089 particles, calling pdeellip() makes Matlab run out of memory. Strange. I'll try Mathematica and see if it's better. –  Chong Luo Oct 26 '11 at 17:08
$10^3$ particles should be no challenge; $10^6$ might be a challenge. I don't use Matlab as regularly as Mathematica, so I cannot help you. But you could post a question on a Matlab forum, and get quick expert advice. –  Joseph O'Rourke Oct 26 '11 at 18:17
I found Mathematica can handle $10^3$ particles quite easily, and produce nice graphs. I'll just use Mathematica. Thanks a lot! –  Chong Luo Oct 29 '11 at 10:33
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