Regarding minimization of edited structures


#1

Dear admins,

Supposing that we have a minimized structure with GROMACS, I wondered if a second minimization is necessary when we e.g. change a residue in a protein. I would like to know if this case is different between the types of organics biomolecules (e.g. in proteins, nucleic acids, lipids). Thank you in advance.


#2

Hi Panos,
Yes, you should minimize every time you do such change in the modelled system. Sometimes you might be able to get along with more careful MD but in general since minimization doesn’t take a long time anyway you won’t gain anything of skipping it.