[gmx-users] Harmonic potential

mn2 at hw.ac.uk mn2 at hw.ac.uk
Thu Mar 24 17:21:37 CET 2005

Hi All,

I have been trying to apply harmonic potenitial on water molecules in a 
slab using umbrella sampling of the pull code. When I leave the 
reference_group blank the programme gives me "Fatal error: Can't find group 
in the index file". But manual(3.2.1)says that if I leave the 
reference_group blank umbrella sampling can be performed in absolute 
coordinate which I wanted to do.Strangley, when I put reference_group=HOH 
in parameter file, it works fine.

Could anyone please explain where things went wrong?

With regards,


On Sat, 25 Dec 2004 11:41:50 -0800 (PST), Michael Brunsteiner 
<mbx0009 at yahoo.com> wrote:

> > > 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.
> michael
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