[gmx-users] Harmonic potential

[David van der Spoel]

On Wed, 2004-12-22 at 00:37 +0000, M.Naser wrote:
> Thanks David.
> 
> I have been wondering how I am supose to specify the molecules in the 1st
> layer.
> 
you pick them by hand, or using your own program.

> With regards,
> 
> Abu
> 
> > On Tue, 2004-12-21 at 18:52 +0000, M.Naser wrote:
> >> Hi David,
> >>
> >> 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
> >>
> >> With best regards,
> >>
> >> Abu
> >>
> >> > On Tue, 2004-12-21 at 15:30 +0000, M.Naser wrote:
> >> >> Hi All User,
> >> >>
> >> >> Could anyone please tell me the way I can apply harmonic potential in
> >> >> water slab.
> >> >>
> >> > please be more specific.
> >> >
> >> >> With regards,
> >> >>
> >> >> Abu
> >> >>
> >> >>
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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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> >>
> >>
> >>
> >> ________________________________________________________________
> >>
> >> DISCLAIMER:
> >>
> >> This e-mail and any files transmitted with it are confidential
> >> and intended solely for the use of the individual or entity to
> >> whom it is addressed.  If you are not the intended recipient
> >> you are prohibited from using any of the information contained
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> >> Watt University does not accept liability or responsibility
> >> for changes made to this e-mail after it was sent, or for
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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
> > ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> >
> > _______________________________________________
> > gmx-users mailing list
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> >
> 
> 
> 
> ________________________________________________________________
> 
> DISCLAIMER:
> 
> This e-mail and any files transmitted with it are confidential
> and intended solely for the use of the individual or entity to
> whom it is addressed.  If you are not the intended recipient
> you are prohibited from using any of the information contained
> in this e-mail.  In such a case, please destroy all copies in
> your possession and notify the sender by reply e-mail.  Heriot
> Watt University does not accept liability or responsibility
> for changes made to this e-mail after it was sent, or for
> viruses transmitted through this e-mail.  Opinions, comments,
> conclusions and other information in this e-mail that do not
> relate to the official business of Heriot Watt University are
> not endorsed by it.
> ________________________________________________________________
> _______________________________________________
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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
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++