Christian Seifert wrote:
Hi!
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?
No, frozen groups, constraints and restraints are distinct concepts in
GROMACS - they imply the use of different algorithms. One is asking for
trouble when one is treating any atom with more than one of these.
Am Dienstag, 27. Oktober 2009 um 17:23 schrieb Jennifer Williams:
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?
(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.
grompp probably lists the number of the various sorts of interactions -
or at least gmxcheck will do so when comparing .tpr generated with and
without frozen groups.
Mark
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