I have created a handful of small molecule candidates and I want to perform MD simulation what basis set should I use to optimize their structures? if it's possible could you provide the DOI of the article which have done the study and optimization?
thank you in advance.
For initial optimization, you could start with PBE-D and the DZP basis set. or TZP if it is a small molecule
I have optimized them using MM and conformation search. I want to optimized them further. well in this case what would you recommend.
If the only goal of the geometry optimization is to prepare files for MD or molecular docking then optimizing at the DFT level does not make any sense. It is very likely, particularly for ligands interacting with proteins / other biomacromolecules that the conformation of the ligand optimized at the DFT level (without the biomacromolecule) will be completely different from the biomacromolecule-bound conformation. Hence this step is completely unnecessary.
Thank you for your response!
what parameters of molecule geometry are changed during the MD? for docking AFAIK only the dihedral angles are changed. so If the length and angle of bonds and charge density and other properties are optimized before performing docking the outcome docking is more reliable.
You can visit the following papers for optimization of any nanostructures prior to any measurements in MD simulations study.
1. https://www.sciencedirect.com/science/article/pii/S0360319922038228?dgcid=coauthor
2. https://www.sciencedirect.com/science/article/abs/pii/S0008622317309314?via%3Dihub
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