If I want to calculate molecular dynamics (Gromacs), do I first need to optimize the geometry of the molecule? For example, I first draw the molecule in Avogadro, and then what? I guess I can't run the molecular dynamics calculation right away? Then should I do the geometry optimization first with, for example, Orca?
its prefer to get your molecule coordinate from available database and use as it but if you choose to draw then yes optz your structure first in avogadro then in any dft software opt.next prepare your python scripts thats include you FF of your system for MD.
Noor Alomari
Thank you! I didn't find any structures in the databases, that's why I choose to draw. Could you clarify this stage, please: "next prepare your python scripts that include you FF of your system for MD"? This is not related to the preparation of the molecule, right?
Thats right ,Its not related to the preparation of the molecule.
its meant for your gromacs MD ,you will use the coordinate of the prepared molecule and add its force field ,angles ..ect
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