[gmx-users] Harmonic potential

Michael Brunsteiner mbx0009 at yahoo.com
Sat Dec 25 20:41:50 CET 2004

> > Thank you very much for your response.I have a protein in a water slab
> > which is placed in a vacuume. When I ran 1 ns run the water drifted away
> > from the slap into the vacumme which I did not want. I have wondering
> > whether I could apply harmonic potential in the water slab to stop
> > drifting water when I go for longer run. Could you please advise me how to
> > apply harmonic potential in water slab or anyother way I can tackle the
> > problem?
> Sorry, that's not implemented, the only thing you could try is position
> restraints in the Z dimension for the outer layer of water

as a workaround you could use umbrella sampling as implemented
in the pull code, this comes basically down to applying a harmonic
potential to a group of your choice. You can ignore the output
in the pull.pdo ...
However, if your water slab is thick enough it should not disintegrate
at all, and if occasionally one or a few single water molecules
drift away from your slab that shouldn't much of a difference ...
If the slab does disintegrate entirely then you should check your
system and settings because something else might go wrong there.


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