[gmx-users] ANY information about pull simulations needed!

[Semen Esilevsky]

Dear gmx users,
Let me ask in such a way:
Did somebody ever used pull simulations to measure the
force acting on a fixed group? Did somebody know at
least something beyond the manual about this type of
simulations?
I'll deeply appreciate ANY comments, ANY references,
ANY relevant information...

Thank you in advance,

Semen


--- Semen Esilevsky <yesint4 at yahoo.com> wrote:
> Dear gmx users,
> since there where no responces to my last posting,
> I'll try again: 
> Could somebody explain how to set-up the constrained
> pull simulations correctly? I've got strange
> results:
> the force doesn't depend on the relative positions
> of
> the monitored molecules and simply oscillates around
> zero with rather large period. 
> I'll be extremely grateful for any suggestions.
> 
> Sincerely,
> Semen Yesylevskyy
> 
> --- Ruben Martinez Buey <ruben at akilonia.cib.csic.es>
> wrote:
> > > Dear Bert,
> > 
> > Thanks a lot four reply.
> > 
> > > >
> > > > Average projection (mean):
> > > > eigenvec 1: -0.365220            0.457450
> > > > eigenvec 2:   0.137630          -0.169460
> > > > eigenvec 3:   0.137790          -0.319940
> > > > eigenvec 4:   0.068647          -0.078291
> > > > eigenvec 5:   0.087228            0.040858
> > >
> > > hmm, I suppose the two trajectories had a
> > different length? Since
> > > otherwise the projections should be symmetrical
> > with respect to zero.
> > > ( ie -0.3   0.3 etc)
> > 
> > They must be exactly symmetrical with respect to
> > zero?
> > I mean -0.40976 and 0.41711 for example is right?
> > 
> > I´ve generated 500 structures in each run with
> > CONCOORD, and then just merged them.
> > Thanks a lot again four your help
> > Regards,
> > Ruben
> > 
> > 
> > 
> > >
> > >
> > > Bert
> > >
> > >
> >
>
____________________________________________________________________________
> > > Dr. Bert de Groot
> > >
> > > Max Planck Institute for Biophysical Chemistry
> > > Theoretical molecular biophysics group
> > > Am Fassberg 11
> > > 37077 Goettingen, Germany
> > >
> > > tel: +49-551-2011306, fax: +49-551-2011089
> > >
> > > email: bgroot at gwdg.de
> > > http://www.mpibpc.gwdg.de/abteilungen/071/bgroot
> > >
> >
>
____________________________________________________________________________
> > >
> > > _______________________________________________
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> > > gmx-users at gromacs.org
> > >
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> > 
> > --
> > ___________________________________________
> > 
> > Rubén Martínez-Buey. PhD student
> > Protein Function and Structure Dept. Lab. 352
> > Centro de Investigaciones Biológicas (CIB-CSIC)
> > C/ Velázquez, 144,  28006  MADRID (SPAIN)
> > Tlf: +34-91-561 18 00 ext. 4380
> > Fax: +34-91-562 75 18
> > 
> > 
> > 
> 
> 
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