[gmx-users] Harmonic potential

[mn2 at hw.ac.uk]

Hi All,

I posted an email regarding umbrella sampling. I did not get any reply. I 
am trying again. I wanted to apply harmonic potential with reference to 
absolute cordinate.I was not able to run the programe leaving the 
reference_group blank. Probably, there is a bug in it. I have tried using
VERSION 3.1.5_pre1 from CVS  and giving me same error message. 

Is there any other way I can apply harmonic potential in the water slab?


With best regards,

Abu



On Thu, 24 Mar 2005 16:21:37 +0000 (GMT), mn2 at hw.ac.uk wrote:

> 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,
> 
> Abu
> 
> 
> 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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