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My question is concerned with the initial tweaking of two or more different molecules to get the optimized geometry. For example, I have one water molecule and a carbon nanotube with similar length with the water molecule. I have a structure of each of them in a cif or pdb format. I learned that I have to manually position them together at different orientations.

(1) How do I determine which among the different orientations has the "most" optimized geometry? (2) Also, does it mean that all orientations are valid if all of them reached minimum energy (given that the approach or technique is correct)? I am thinking my method will involve using LAMMPS for minimization of the various orientations and then further structure relaxation using a QM code such as Quantum Espresso.

Thank you! Let me know if anything does not make sense.

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  • $\begingroup$ +1. Welcome to our community! $\endgroup$
    – Camps ♦
    Commented Sep 4 at 13:08
  • $\begingroup$ @Camps Thank you so much! $\endgroup$
    – Jay V.
    Commented Sep 4 at 18:07

1 Answer 1

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Answering your questions:

  1. To create the startup conformation, I recommend using the Docking Submodule (aISS) implemented in the xTB package. It will screen for the best complex formation (see below).
  2. No, not all orientations are "valid". In general, optimizing from a given initial conformation can take the system to a local energy minimum instead of a global energy minimum in the potential energy surface. A method like aISS, will screen the potential energy surface in order to find a global energy minimum.

About the aISS method:

The principal idea of aISS is to find the energetically lowest structure (global energy minimum) of the largest interaction between two given fragments, which often has a dominant impact in the real system. A few energetically higher structures (per default 15) are also obtained by the algorithm and optionally, a more complete ensemble of thermally populated structures can be generated. As the possible bonding motifs and geometrical structures can be rather diverse and complex, multiple steps applying different approximations are performed during an aISS run.

The workflow is shown in the figure below:

All the information about the aISS method are in the published paper:

  • Christoph Plett and Stefan Grimme, Automated and Efficient Generation of General Molecular Aggregate Structures, Angew. Chem. Int. Ed. 62, e202214477 (2023). DOI 10.1002/anie.202214477 (Open Access)

The xTB package can be downloaded from Github repository:

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  • $\begingroup$ This is a very interesting suggestion. I have tried to install xTB on my Windows machine, but I am having difficulty either using cmake or conda as they both resulted in errors. I am not sure about the learning curve of using the software either. However, can you suggest another way to screen the best complex formation? Can you also share any link or tutorial on installing xTB on Windows? $\endgroup$
    – Jay V.
    Commented Sep 4 at 18:11
  • $\begingroup$ There is no need to compile on Windows. There are pre-compiled executables in the Github repository. The learning curve is smooth, very easy to follow the examples on the documentation page. $\endgroup$
    – Camps ♦
    Commented Sep 5 at 11:42
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    $\begingroup$ Thank you, @Camps. I was able to install xTB and used the geometry optimization feature, specifically the aISS feature you mentioned. I will definitely consider this. $\endgroup$
    – Jay V.
    Commented Sep 9 at 6:05

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