[gmx-users] pulling

[aherz]

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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