Hello all, I am using amber99SB to model an antibody with organic ligands.
I know we could choose to restrain all atoms or only heavy atoms during the equilibration. But I wonder if this really matters for my system. As far as I know, equilibration is aimed at getting the temperature and pressure right, mainly for the solvent. And as long as we are going to do a 'real' MD production run without restraints, it should not matter too much how we restrained the antibody and ligands? I am not if I am right about this. Any suggestions? Thanks, Yun
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