[gmx-users] cvs version and position restraints...
vaiana at physik.uni-bielefeld.de
Mon Jul 21 14:31:19 CEST 2008
yes, it was an older version. And I did have separate pme nodes when
posre was working. So now I'm trying out the new CVS version.
On Jul 21, 2008, at 1:53 PM, Berk Hess wrote:
> There was a bug with PME and position restraints in the CVS version,
> but that has been fixed a month ago. This bug has exactly the behavior
> you describe, posres should work ok with separate pme nodes (nnodes
> >= 12),
> but not without (1 < nnodes < 12).
> So I assume you are not using the most recent CVS version?
> > Date: Tue, 15 Jul 2008 18:17:10 +0200
> > From: vaiana at physik.uni-bielefeld.de
> > To: gmx-users at gromacs.org
> > Subject: [gmx-users] cvs version and position restraints...
> > Hi everyone,
> > I have a small DNA duplex in a dodecahedron box. Amber forcefield.
> > water. I have position restraints defined for the whole duplex in my
> > topology. I'm running exactly the same input script on 2, 4 and on
> > cpus. The one with 12 produces a trajectory in which it is quite
> > that the restraints are working: the stronger the restraints on a
> > set of atoms, the less these atoms move away from the equilibrium
> > position during the simulation. With 4 and 2 cpus, it is af if no
> > restraints are used (the whole system tumbles and moves around the
> > although I do see energy terms for the restraints in the log file...
> > I'm using the CVS version (downloaded June 4th).
> > I'm not sure but I think I remember someone having a similar
> problem on
> > version 3.2 but I don't remember how/if it was solved. I couldn't
> > anything on the mailing lists.
> > Any clue about what's going on?
> > Thanks,
> > Andrea
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