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

Mark Abraham Mark.Abraham at anu.edu.au
Mon Oct 31 13:08:44 CET 2011

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 


> I am not if I am right about this. Any suggestions?
> Thanks,
> Yun

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