[gmx-users] Re: pulling

Fri Jul 31 12:56:30 CEST 2009

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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