[gmx-users] Freezing a molecule

Jennifer Williams Jennifer.Williams at ed.ac.uk
Tue Oct 27 17:23:06 CET 2009


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?
(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.


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