[gmx-users] Freezing a molecule

Christian Seifert cseifert at bph.ruhr-uni-bochum.de
Wed Oct 28 11:10:40 CET 2009


You are using a "frozen group" but you are not using constraints?!?

As far as I know, a frozen group IS a constrained group. Did you mean 
something different?


Am Dienstag, 27. Oktober 2009 um 17:23 schrieb Jennifer Williams:

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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M.Sc. Christian Seifert
Department of Biophysics
University of Bochum
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