[gmx-users] temperature scaling and frozen atoms

m b mic0404 at yahoo.com
Wed Jul 30 20:46:01 CEST 2003

dear Xavier,

Thanks for your answers.
Indeed I did try to set the target
temperature of the crystal (the frozen part)
to a finite value ... no difference.
Using restraints (harmonic potentials) instead of
constraints is probably no good idea since I would
have to use a very large force constant and
probably that would mean a shorter time step.
I exclude the interactions beneath the frozen
atoms in order to gain speed. Thus, if
If I use a small force constant the positions
of the atoms in the crystal would be rather arbitrary
since they do not interact with each other. Letting
them interact would again result in a speed penalty.

However, I did manage to get it working,
There are two things one has to do:
1) never set the center of mass motion to zero
(no problem if the comm is zero or close to zero
at the beginning of the simulation)
2) don't define two seperate temperature scaling
groups for the frozen and the not frozen parts but
only one (the entire system).

If both of the above conditions are given it works,
strange, isn't it ?
The system would not explode anymore and the dynamics
looks reasonable. I am still a bit concerned, however,
about whether the EOM are solved correctly with this
setup and whether the temperature of the non-frozen
part given in the output is really correct.

best wishes

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