[gmx-users] Freezing a molecule
Mark.Abraham at anu.edu.au
Wed Oct 28 12:42:37 CET 2009
Christian Seifert wrote:
> 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:
> 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.
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