[gmx-users] Restarting minimization

[Justin Lemkul]

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

-- 

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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540)
231-9080http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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