GROMACS version: 2020.1
GROMACS modification: Yes
Hello, I wanna ask a question so I have done RMSD, RMSF, Rg and HBond analysis and found this graph as the result
So I have found Isoeugenol with yellow line have a lower RMSD value and also RMSF value “BUT” have a higher Rg score and also no HBond has been found
But elemicin with a blue line have a lower Rg score and 2 intermolecular HBond
But for note the low Rg score because the tail was folded during 100-ns simulation.
So I wanna ask which one is the most suitable one to fit at the enzyme’s active site?
and also this enzyme in nature, the active site was found had a hydrophobic condition
Thanks a lot