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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