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

[Frauke Meyer]

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)
> > > 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