Hi! I was wondering if it is possible to make a cluster out of two small organic dye molecules by using Avogadro or some other free licensed program for ligand optimization. I have heard that it may be done in Gaussian when they put the two structures closer and somehow the program calculate the best pose for cluster formation. But I have no experience in any of it.
Hello!
Are you set up for calculations on a server? What level of theory do you want to have (MM, Semiempirical, DFT, etc.)? Avogradro is just the Graphical User Interface for creating and analyzing results, similar to the paid program GaussView. I use GaussView to create calculations and observe the results, but the calculations themselves are done on Gaussian, running on a server (ORCA and GAMESS are other software for running the actual calculations, ORCA is free i think).
You can bring two molecules close together in Avogadro, then you would need to run the calculation using ORCA or similar on a server (or a person computer if very low level) to get the optimized geometry and energy. You would want to optimize the monomer too if you want the energy of the dimerization:
2 Monomer --> 1 Dimer
Sincerely,
Kyle
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