[gmx-users] Restarting minimization

Justin Lemkul jalemkul at vt.edu
Sat Apr 6 20:37:21 CEST 2013

On Sat, Apr 6, 2013 at 2:23 PM, Juan Antonio Raygoza Garay <raygozag at psu.edu
> wrote:

> Hi, i'm new to grimaces and want to run a minimization process in parts,
> but i'm having problems extracting the last frame, when i try the following
> command:
> trjconv -s em-vac${ID}.tpr -f em-vac${ID}.trr -o mintmp.pdb -e 0
The last frame is always written by mdrun when the process completes.
Moreover, your command will extract the first frame (-e 0 is "ending at
zero time), not the last.

> it returns no data, if i try 11 in the frame number it prints out  a
> model, but when trying to run mintmp.pdb, i get the following error:
> Fatal error:
> There is no domain decomposition for 8 nodes that is compatible with the
> given box and a minimum cell size of 23.38 nm
> Change the number of nodes or mdrun option -rdd
> Look in the log file for details on the domain decomposition
> what am i doing wrong? or is there a tutorial where someone does this.
Intermediate frames that are stored in trajectories have molecules broken
across periodic boundaries. In principle, that shouldn't be an issue, but
the error message suggests that's precisely the problem. trjconv -pbc mol
will take care of that problem. Domain decomposition cells should be on the
order of the largest cutoff.




Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540)


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