Bert de Groot
bgroot at gwdg.de
Tue Mar 4 16:56:26 CET 2003
Anton Feenstra wrote:
> I can see four possibilities:
> 1) no scaling (current implementation)
> 2) 'normal scaling': frozen coordinates scale like normal ones
> 3) COM scaling: COM of frozen groups 'scale' along with normal coordinates.
> 4) group scaling: COM remains frozen, group 'size' is scaled.
> I don't know if option 4 makes sense, it seems it might be useful for
> some systems where a large group (protein?) should remain in a fixed
> conformation and fixed location (in a bilayer), without the pressure
> scaling distorting the interface between frozen and normal atoms.
but then you'd distort the geometry instead?
> While we're at it, we don't yet have an option to freeze *only* the
> COM of a group, do we? That might be handy also.
wouldn't that be the same as normal group-COM motion removal?
What would be useful in some cases (e.g. for determining a potential of
mean force) is 1/2D COM removal of a group. But since I'm not familiar enough
with that part of the source I'm rather reluctant to start on such an
implementation myself, and could merely put it on my wish-list.
> After reading the gmx-users discussion (between Berk & Bert), I wonder
> if it isn't possible to add additional constraints for the 1/2D frozen
> particles, which would not allow them to move in 1/2D during constraints
I don't know if it would be practicable, but I don't see an obvious reason
why it couldn't work in principle (there is a solution to the applied constraint;
Shake might need more iterations to find it, I don't know about lincs).
Dr. Bert de Groot
Max Planck Institute for Biophysical Chemistry
Theoretical molecular biophysics group
Am Fassberg 11
37077 Goettingen, Germany
tel: +49-551-2011306, fax: +49-551-2011089
email: bgroot at gwdg.de
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