[gmx-users] Re: pulling

Berk Hess gmx3 at hotmail.com
Wed Aug 5 15:38:05 CEST 2009 

You really need pull_pbcatom0, since your slab is thicker than
half the box you otherwise can have periodicity errors.

Berk

> Date: Wed, 5 Aug 2009 15:27:06 +0200
> From: alexander.herz at mytum.de
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Re: pulling
> 
> 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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