[gmx-users] Harmonic potential
mn2 at hw.ac.uk
mn2 at hw.ac.uk
Sun Mar 27 22:00:05 CEST 2005
Hi David,
Thank you very much for your quick reply.Sorry for confusing you. I meant
any other way apart from pull code.Will it be very difficult to add my own
code to gromacs?
With best regards,
Abu
On Sun, 27 Mar 2005 21:48:41 +0200, David van der Spoel
<spoel at xray.bmc.uu.se> wrote:
> 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
> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
>
> --
> 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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