[gmx-users] cvs version and position restraints...

Berk Hess gmx3 at hotmail.com
Mon Jul 21 13:53:35 CEST 2008


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. Spce 
> 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 12 
> cpus. The one with 12 produces a trajectory in which it is quite clear 
> that the restraints are working: the stronger the restraints on a given 
> 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 box), 
> 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 find 
> anything on the mailing lists.
> Any clue about what's going on?
> Thanks,
> Andrea
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