I am doing simulated annealing on a few guanine molecules, but when I see the generated structure after simulation, each molecule is planar, but they are all non planar related to each other. I know they should be planar because QM calculations show them as planar. I was wondering if I should add any keyword in order to keep them planar?
What software are you using? LJ and electrostatic parameters are generally used for intermolecular forces. I guess you could add one, but it would limit you to that specific conformation. Maybe you could optimize at pm6 or b3lyp/6-31G* to check. Also how strong should the improper torsion be?-you would be guessing at best.
I do not think you understand my question completely, I meant 2 referent guanines, I want them to be planar, I know I should add it in my frcmod file,
Sorry i am unfamiliar with the term 'referent'. Does that mean that they are neighboring Guanosines on a chain? Could you include a picture? with frcmod files, I assume you are using amber?
Also I think it will be complicated because the guanines are probably in different molecular groups. The topology file builder (tleap in Amber) may not correctly add the improper dihedral, and you may have to edit the topology directly (which is a pain).
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