Thanks Berk,
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.
Andrea
On Jul 21, 2008, at 1:53 PM, Berk Hess wrote:
Hi,
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?
Berk.
> Date: Tue, 15 Jul 2008 18:17:10 +0200
> From: [EMAIL PROTECTED]
> To: gmx-users@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
>
>
> _______________________________________________
> gmx-users mailing list gmx-users@gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> 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 [EMAIL PROTECTED]
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Express yourself instantly with MSN Messenger! MSN Messenger
_______________________________________________
gmx-users mailing list gmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
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 [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
_______________________________________________
gmx-users mailing list gmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
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 [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
