Energy minimization with flexible water

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GROMACS version:2018
GROMACS modification: No
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Hi, I would like to perform an energy minimization of my simulation system. In few tutorials I have seen that people advice to use flexible water molecules using define=-DEFLEXIBLE in em.mdp file for the energy minimization purpose and after that for further equilibration apply constraint on water molecules. As far as I know that water models are rigid by nature. For example I am using tip3p water model. So, is it better if we do energy minimization with flexible water to stabilize the system more for further equilibration where we will apply SETTELE constraint algorithm? flexible or rigid water any of them is fine for the energy minimization purpose?

my systems consist of: 1) protein+water+urea+ions and 2) binary mixture of ethanol & water

any help is much appreciated, thank you

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If you make water flexible, you should do another round of minimization with the waters held rigid, because that’s how they will be treated during dynamics. Water molecules can distort and make subsequent simulations unstable. FWIW, I have never found flexible minimization to solve anything other than to show me where a bad contact was by badly distorting one or more water molecules.