[gmx-users] Freezing a molecule

ilona.baldus at bioquant.uni-heidelberg.de ilona.baldus at bioquant.uni-heidelberg.de
Tue Oct 27 19:54:07 CET 2009

Quoting Jennifer Williams <Jennifer.Williams at ed.ac.uk>:

> Hello,
> One quick questions...
> I have a structure for which I now want to freeze a portion.
> I already have a .top file where the entire structure is flexible (bond
> angles, stretches and torions defined).
> When freezing, do I need to delete all those bond stretches, angles and
> torsions associated with the frozen part from my .top file?

No. Just select the freeze group and say yes ("Y") in the directions  
you want your molecule to be frozen (in the mdp-file). I also choose  
an energy_group exclusion for the frozen part, though I don't know  
whether that's necessary.

> (I am not using constraints on the frozen portion as I have seen this
> can cause problems).
> Will the bonding parameters all be set to zero when the these atoms are
> frozen or will their contribution be calculated if I leave these terms
> in.
> Thanks
> -- 
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