[gmx-users] distance restraints and lincs warning

[Kai Zhuang]

i'm using 3.2.1

I'm bound by confidentiality agreement... can't send you the structure file :-(

one possible source of error is that i deleted a ligand from the
original structure file as well as some space filling HETATM groups
(these space fillers are really just space fillers)
is this a possible source of error?

i really just want to find a way to prevent the bond from forming.  is
there any gromacs codes that stops bonds from forming?


On 6/21/05, Anton Feenstra <feenstra at few.vu.nl> wrote:
> A.Rampioni wrote:
> 
> > Dear colleagues,
> >
> > I am performing some simulations on the following system: 3 peptide in a
> > beta-sheet configuration + other 3 peptides in a beta-sheet
> > configuration 1 nm far apart in a truncated octahedron box.
> > I imposed on both the trimers improper dihedral restraints on one
> > peptide and distance restraints among the peptides of the trimer.
> > I want to bring the two trimers close together, so I imposed some
> > distance restraints even between the trimers.
> >
> > I have performed an energy minimization of the starting configuration
> > and a further mdrun with position restraints (without distance
> > restraints) for  10 ps.
> >
> > Then I turn on distance restraints and WITH THE VERSION 3.1.4 EVERYTHING
> > WORKS, BUT WITH THE VERSION 3.2.1 IT DOES NOT WORK !!!
> [...]
> > Any idea of what can be wrong?
> 
> Have you compared different energies (LJ, Coul, disre, etc.) between the
> versions?
> 
> 
> --
> Groetjes,
> 
> Anton
> 
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> |  _   _  ___,| K. Anton Feenstra                                     |
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-- 
Kai Zhuang
BioMedical Engineering @ University of Toronto
kai dot zhuang at gmail dot com
kai.zhuang at gmail.com
6478314789