[gmx-users] Freezing a molecule
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
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