[gmx-users] Re: pulling

Wed Aug 5 15:27:06 CEST 2009

Hm..setting

>>>> > >>> pull_geometry = direction
>>>> > >>> pull_vec1 = 0 0 1
>>>>         
should fix the pbc prob or do I need to set pull_pbcatom0 as well?
Cause it still aint working using these settings (without the
pull_pbcatom0).

Thx,
Alex

Berk Hess schrieb:
> No (completely) frozen groups are treated correctly.
> I had to look in (my own) code again, but for a fully frozen group
> the inverse mass is set to 0 in the pull code.
>
> Berk
>
> > Date: Fri, 31 Jul 2009 12:49:55 +0200
> > From: schlesi at uni-mainz.de
> > To: gmx-users at gromacs.org
> > Subject: [gmx-users] Re: pulling
> >
> > Could it also be possible that 'pull = distance' makes problems because
> > it pulls both groups and here one group is frozen? Only an idea, i have
> > never tried to pull a frozen molecule.
> > Thomas
> >
> >
> > > ------------------------------
> > >
> > > Message: 5
> > > Date: Fri, 31 Jul 2009 12:38:19 +0200
> > > From: Berk Hess <gmx3 at hotmail.com>
> > > Subject: RE: [gmx-users] pulling
> > > To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> > > Message-ID: <COL113-W5604F1D24936CF27D18DFE8E100 at phx.gbl>
> > > Content-Type: text/plain; charset="iso-8859-1"
> > >
> > >
> > > Ah, then you could have a pbc problem for determining the COM of
> the slab,
> > > since you slab is thicker than half the box.
> > > You have to set pull_pbcatom0 to an atom in the middle of the slab.
> > >
> > > pull_init1 doesn't change.
> > > The only thing the geometry change affects is the direction you
> pull in.
> > > With distance you could be unlucky that it takes the distance
> > > in the opposite direction.
> > >
> > > Berk
> > >
> > >> Date: Fri, 31 Jul 2009 12:32:13 +0200
> > >> From: alexander.herz at mytum.de
> > >> To: gmx-users at gromacs.org
> > >> Subject: Re: [gmx-users] pulling
> > >>
> > >> Thx for the quick reply!
> > >>
> > >> I use 4.0.5, pbc z=yes
> > >> Box height = 17.5nm
> > >> gld slab is from z=0 to z= 9.5;
> > >> So distance=5.5 should give 1.0nm above surface right?
> > >>
> > >> What do I have to put for pull_init1 if i use direction??
> > >>
> > >> Thx,
> > >> Alex
> > >>
> > >> Berk Hess schrieb:
> > >>> Hi,
> > >>>
> > >>> I hope you are using 4.0.5, I fixed several bug in the pull code for
> > >>> older 4.0 versions.
> > >>>
> > >>> The problems you are seing could be due to pbc.
> > >>> Do you have pbc in Z, and what is the height of your box?
> > >>>
> > >>> A safer setup is:
> > >>> pull_geometry = direction
> > >>> pull_vec1 = 0 0 1
> > >>> But they should give the same answers if you do not have pbc issues.
> > >>>
> > >>> Berk
> > >>>
> > >>>> Date: Fri, 31 Jul 2009 12:13:07 +0200
> > >>>> From: alexander.herz at mytum.de
> > >>>> To: gmx-users at gromacs.org
> > >>>> Subject: [gmx-users] pulling
> > >>>>
> > >>>> Hey,
> > >>>>
> > >>>> I appear to have serious trouble understanding how to set up
> the pulling
> > >>>> properly.
> > >>>>
> > >>>> I have many configurations of a protein partially adsorbed to a
> froozen
> > >>>> surface (the configs differ
> > >>>> in the amount of the protein that has been desorbed).
> > >>>> Now I want the pulling to keep the distance of the desorbed end
> of the
> > >>>> protein to the surface using the harmonic pot.
> > >>>> Now the documentation is not very clear how this all works so I ran
> > >>>> several experiments to figure it out but I failed.
> > >>>> I use the following options:
> > >>>>
> > >>>> ;PULLING
> > >>>> pull = umbrella
> > >>>> pull_geometry = distance
> > >>>> pull_dim = N N Y
> > >>>> pull_nstxout = 1000
> > >>>> pull_nstfout = 1000
> > >>>> pull_ngroups = 1
> > >>>> pull_group0 = GLD
> > >>>> pull_group1 = ASN
> > >>>> pull_vec1 = 0.0 0.0 0.0
> > >>>> pull_init1 = 5.27778
> > >>>> pull_rate1 = 0.0
> > >>>> pull_k1 = 100
> > >>>>
> > >>>>
> > >>>> where gld is the surface and asn is the end residue of the
> protein and
> > >>>> pull_init1 is set to the desired COM distance of the two
> > >>>> groups (gld is froozen). I use the same settings for all runs, only
> > >>>> changing pull_init1 to get the desired distance.
> > >>>> Now for some reason using this setup either pulls the ASN end
> of the
> > >>>> protein completely onto the surface or very far away from it
> depending
> > >>>> on the value I use for pull_init1.
> > >>>> So the distance between what and what shall I put for
> pull_init1? What
> > >>>> else is wrong?
> > >>>>
> > >>>> Thx,
> > >>>> Alex
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