[gmx-users] position restraints on heavy atoms or all?

Yun Shi yunshi09 at gmail.com
Sun Oct 30 02:04:19 CEST 2011

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?

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