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

[Frauke Meyer]

Dear Semen,
> Thank you very much for reply! I began to think that
> this type of simulations is never used ;)
>
Might be.
> 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...
>
Pull Type "afm" is surely not buggy in the 3.1.4 version. What about
testing your setup in the following way: You change oull type to afm,
choose a velocity that is about the average of the one you observe in the
free MD (I assume, the ion is freely moving into the channel, as you
expect forces in this direction), and choose a stiff spring.
Then you look onto the force that changes with spring position and check
if this makes sense. It this also does not work fine, your setup is
somehow wrong.

Cheers,
Frauke


 > 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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> > > > > --
> > > > > ___________________________________________
> > > > >
> > > > > Rubén Martínez-Buey. PhD student
> > > > > Protein Function and Structure Dept. Lab. 352
> > > > > Centro de Investigaciones Biológicas
> > (CIB-CSIC)
> > > > > C/ Velázquez, 144,  28006  MADRID (SPAIN)
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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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--
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