[gmx-users] still pull probs

aherz alexander.herz at mytum.de
Mon Aug 17 17:57:26 CEST 2009

Hi guys,

I'm back from my holidays and looking at the results which have
accumulated since, the pulling still doesn't do what I want it to do.
(this is a follow up to my earlier problems)

So the system is a fragment of spider silk (with an ASN group at the
end) which has been adsorbed onto a crystal surface.
Afterwards the ASN group is supposed to be pulled to a certain distance
of the surface and then stay there
(so we get into TD equilibrium).
I've attached both the gro and the mdp file of the input files which are
supposed to accomplish the second part (note, only the mdp file is attached as
the list rejects mails >50kb).

They way I think it should work is that the distance between the COM of
the ASN group and the COM
of the GLD group (which should be the middle between the two gold slabs
which make up the surfaces)
should be held more or less constant due to the harmonic potential
between the two.
The pbcatom0 is set to an atom in the top most layer of the upper gold slab.
The gold is still froozen and there are pbc in all 3 dim.

The input files I have attached cause the ASN group to be pulled to the
very top of the sim box
(having a distance much bigger than the 7.7nm (init_vec in the mdp) when
looking the original sim box).

So what on earth am I doing wrong??

I'd be really thankful for some more help.

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