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

[Semen Esilevsky]

Thank you very much for reply! I began to think that
this type of simulations is never used ;)

I've tried to simulate the ion channel and the ion
sitting somewhere on the pore axis. The goal is to
measure the force acting on the ion in each point on
the pore axis i.e. to obtain a force profile (or
energy profile after integration). The ion is a pull
group. The whole channel protein is a reference group.
Pull type is "constrained" along z-axis (pore axis).

The channel pore is charged and it HAVE TO be an
attraction, which pulls the ion into the channel (if
it is placed near the mouth). This force obviously
have to be distance-dependent. 

What I have is an oscillating (in time) force centered
at zero regardless of the ion position. A kind of
quasi-periodical noisy sinusoidal...

I have absolutely no idea what is wrong. Normal MD
runs smoothly on this system. Probably it is a bug?

Semen

--- Frauke Meyer <fmeyer at ix.urz.uni-heidelberg.de>
wrote:
> Dear Semen,
> > 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...
> >
> I have not done a pulling simulaion to calculate the
> force on a fixed
> group, but on a group dislocated with a chosen
> pulling velocity.
> The cvs pull code is buggy, but the 3.1.4 code is
> fine, but can not be
> run in parallel.
> I am not sure if I can help you - what are your pull
> parameters, what is
> your pull group?
> 
> Frauke
> 
> > 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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> > > > >
> > >
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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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> 
> --
> Frauke Meyer
> Drug Discovery and Design Center
> Shanghai Institute of Materia Medica
> 555 Zu Chong Zhi Road, Zhangjiang Hi-Tech Park
> Shanghai 201203
> Tel: +86 21 50806600*1201, Fax: +86 21 50806600*1205
> http://www.dddc.ac.cn,
> e-mail:frauke.meyer at mpi-bpc.mpg.de
> 
> 
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