[gmx-users] distance restraints and lincs warning
feenstra at few.vu.nl
Tue Jun 21 17:48:28 CEST 2005
> 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
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