On 30/10/2011 11:04 AM, Yun Shi wrote:
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?
Initial velocities are sampled from a theoretical distribution. Initial
positions can be quite unphysical from whatever process created them -
particularly hydrogen atoms. These can combine poorly in the absence of
some sensible restraints. Only you can assess the quality of your input
model.
Mark
I am not if I am right about this. Any suggestions?
Thanks,
Yun
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