GROMACS version: 2025.4
GROMACS modification: Yes/No
I am working with Chalcones as ligand with protein. Initially these chalcones are in trans confirmation. One of the chalcone derivative becomes cis after NVT step. For trans to cis change bond breaking and formation should take place. Which is most unlikely to happen in real system. What parameters should be changed in NVT.mdp so that this will not happen else is there any good reason as in why it might be happening ?