[gmx-users] Harmonic potential
David van der Spoel
spoel at xray.bmc.uu.se
Sun Mar 27 22:05:12 CEST 2005
On Sun, 2005-03-27 at 21:00 +0100, mn2 at hw.ac.uk wrote:
> 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?
If you run on a single processor you can quite easily hack the position
restraints code in src/gmxlib/bondfree.c
>
> 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
> > > > >
> > > > >
> > > > >
> > > > >
> > > > >
> > > > > __________________________________
> > > > > Do you Yahoo!?
> > > > > Meet the all-new My Yahoo! - Try it today!
> > > > > http://my.yahoo.com
> > > > >
> > > > >
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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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--
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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