[gmx-users] Harmonic potential

David van der Spoel spoel at xray.bmc.uu.se
Sun Mar 27 22:16:15 CEST 2005


On Sun, 2005-03-27 at 21:15 +0100, mn2 at hw.ac.uk wrote:
> Thank you david. Did you mean non parallel or single processor parallel? I 
> have just updated (using the command cvs update) and recompiled, still 
> having same problem?
Sorry what problem?
> 
> With regards,
> 
> Abu
> 
> On Sun, 27 Mar 2005 22:05:12 +0200, David van der Spoel 
> <spoel at xray.bmc.uu.se> wrote:
> 
> > 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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> > 
> 
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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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