Well, enough of talk about non-scientific thinking. There is something about which I have wondered many times. The steps in doing any MD is as follows : Assign charges, atom type (sp3, sp2 etc with variations) and Van der Waals radii to each atom. Based on this, the parameters will be decided. As of now, most force fields use fixed charges which means their value does not change based on the environment. So, protonation states of His and others have to be determined empirically at this step. Following the parameter assignment to each atom, bond and torsion (together they constitute a force field), all short contacts etc need to be removed. Now, at this point, you place waters randomly around your protein and then 'energy minimize' your structure which relieves short contacts between waters and the protein. You can keep all atoms of the protein fixed, or allow some relaxation to take place at this step. Now, once the protein is ready (BTW, this is what is c...