[gmx-users] Constrained pull simulations

[Semen Esilevsky]

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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> --
> ___________________________________________
> 
> 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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