Hello all,<br>
<br>
I am using amber99SB to model an antibody with organic ligands.<br><br>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?<br>
<br>
I am not if I am right about this. Any suggestions?<br>
<br>
Thanks,<br>
Yun