[gmx-users] energy minimization settings

[Lei Zhou]

Dear gmx-users,

I am doing a simulation with a protein-ligand system. According to
standard protocol, there should be energy minimization (EM) steps
before and after adding ions. Should I do positional restrain on
protein-ligand (put define= -DPOSRES into em.mdp file), or just use
flexible water (put define= -DFLEXIBLE into em.mdp file, with
positional restainr) during both
EM steps? If I don't restrain the position of protein-ligand, will the
EM change the starting structure?

Should I set constraints on all-bonds during EM?

I saw some people using flexible water here. What is the reason for that?

For the two EMs, should I use steep for both or use steep + cg?

Thanks in advance.

Lei Zhou