[gmx-users] pulling

[Berk Hess]

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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