[gmx-users] Harmonic potential

[David van der Spoel]

On Sun, 2005-03-27 at 22:09 +0100, mn2 at hw.ac.uk wrote:
> 
> Hello again David,
> 
> Thank you very much for your reply. Could you please give me an idea how 
> complex will it be to add the parallel?
If you want to keep the center of mass of your water slab at a constant
position you will have to compute the partial centers of mass on each
processor and the  communicate and sum these. Not very complicated to do
in an ad-hoc way.
> 
> With best regards,
> 
> Abu
> 
> 
> 
> On Sun, 27 Mar 2005 23:00:55 +0200, David van der Spoel 
> <spoel at xray.bmc.uu.se> wrote:
> 
> > On Sun, 2005-03-27 at 21:36 +0100, mn2 at hw.ac.uk wrote:
> > > Hi David,
> > > 
> > > I have been trying to apply harmonic potential with reference to
> > absolute 
> > > coordinate using an option umbrella sampling  in pull conde,on
> > water 
> > > molecule in slab.Probably, there is a bug in pull code as harmonic
> > 
> > > potential without reference goup is not working. I tried code from
> > CVS, it 
> > > gave me error message. You advised me to update the code in cvs
> > and I did 
> > > using the command cvs update. It is still giving me same error
> > message.
> > check instructions for downloading on the website, they should work.
> > the
> > CVS code is not production ready though... use at your own risk.
> > > 
> > > 
> > > I also asked whether I could apply harmomic potential other than
> > pull code 
> > > and you mentioned about hacking position restraints code in 
> > > src/gmxlib/bondfree.c if I run on a single node. I asked you
> > whether you 
> > > meant non parallel running.
> > yes, not parallel. that is, it is just more complex to add the
> > parallel
> > code.
> > > 
> > > 
> > > with best regards,
> > > 
> > > Abu
> > > 
> > > 
> > > 
> > > 
> > >
> > -------------------------------------------------------------------
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> > > 
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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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> 
> 
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> 
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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
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++