[gmx-developers] [gmx-users] freezegroups

Berk Hess gmx3 at hotmail.com
Tue Mar 4 15:44:45 CET 2003


I added comments about constraints and pressure coupling to the freeze group
paragraph in the manual.

Pressure coupling is another problem.
We have talked about this before, but there is no solution yet.
At the moment I need freeze groups where the frozen coordinates scale with
the pressure scaling. But currently the frozen coordinates are not scaled.
Both methods have undesirable effects.
Not scaling preserves the geometry, but can give unwanted effects,
as for instance solvent will be forced to flow around the frozen group
during scaling.
Scaling does not have this problem, but this can distort the geometry of a 
molecule. Also the frozen coordinates might drift in long simulations due
to the numerical precision.

Another option is to pressure scale the center of mass of the frozen parts 
each molecule. But this might be complicated to implement.

Personally I would only need scaled coordinates, but maybe we should 
two options?


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