In the same aspect as some of my previous questions, I am interested in modeling molecules on different surfaces and to study the interfacial effect on them.

One of the most important problems that one can face in such aspect is how to create an initial guess of randomly oriented and distributed molecules over the material surface.

While it is relatively easy to calculate a single molecule on a surface and, if necessary, use Periodic Boundary Conditions to replicate such unit in the material plane, I am not aware in what is the best option to create a much denser 'packing' in a randomized distribution.

Any idea about software or methodology to set this initial structure?

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    $\begingroup$ You want to use Packmol, definitely, which lets you create various random initial packings of molecules - whether on surfaces or in biomolecular simulations. One thing to remember is that molecules on surfaces are rarely perpendicular to the surface plane - there's usually a tilt angle. $\endgroup$ – Geoff Hutchison May 11 '20 at 12:56
  • $\begingroup$ Thanks Geoff, I’ll take a look at such software. :) $\endgroup$ – SalvaCardona May 11 '20 at 12:57
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    $\begingroup$ @GeoffHutchison, you should make that into an answer rather than a comment. $\endgroup$ – taciteloquence May 12 '20 at 4:03

As mentioned by @GeoffHutchison, PACKMOL is probably the most used one for random dense packing of molecules.

Sometimes this might however not suit your needs, e.g. if the shape you want to fit molecules into is not supported by PACKMOL or you want to achieve a certain distance. I achieved good results using the surface tools of ASE. Since it's Python you can create random positions with restraints you choose. Of course you will lack the automatic overlap prevention PACKMOL offers.


If your molecules form not too many types of adsorption complexes on your surfaces, then you can built a lattice model with SuSMoST ( http://SuSMoST.com/ ) and run a short Monte Carlo simulation at high temperature. High temperature Monte Carlo gives you essentially a random structure.


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