[gmx-users] Harmonic potential

[David van der Spoel]

On Sun, 2005-03-27 at 20:34 +0100, mn2 at hw.ac.uk wrote:
> 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?

First, please upgrade to the latest version. Second, you are probably
referring to the pull code, but it's not clear from your question.
> 
> 
> 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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> > >  
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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,          75124 Uppsala, Sweden
phone:  46 18 471 4205          fax: 46 18 511 755
spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,          75124 Uppsala, Sweden
phone:  46 18 471 4205          fax: 46 18 511 755
spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++