[gmx-users] cvs version and position restraints...
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?
> gmx-users mailing list gmx-users at gromacs.org
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Express yourself instantly with MSN Messenger! Download today it's FREE!
-------------- next part --------------
An HTML attachment was scrubbed...
More information about the gromacs.org_gmx-users