[gmx-users] number of DD cells

[Mark Abraham]

On 05/03/11, "Justin A. Lemkul"  <jalemkul at vt.edu> wrote:
> 
> 
> Moeed wrote:
> >Hello,
> >
> >I am attempting to increase the density using NPT. As I increase the pressure to compress the system after some steps simulation crashes. I thought maybe its becasue I am compressing too fast but even when I take a stepwise approach to compress gradually the same error comes up. The density at the point of crash is about 30 SI while I need 650 which is the actual density. Topology file is generated successfully and also I did EM before MD.
> >
> >Initial box size is 30 nm. As suggested in the link below I reduced the size to 20 nm (there are 2500 atoms in the system ) but the same error appears.
> >http://lists.gromacs.org/pipermail/gmx-users/2009-April/041488.html
> >
> >I also tried less -np from 7 to 4 but no success.
> >
> >Can you please tell me what this exclamation mark mean which I get at times in parallel trials.(vol 0.99 !)
> >
> 
> Domain decomposition relies on dividing your system up into reliably-sized domains in order to communicate force, coordinate, energy, etc. information.  If something happens to skew or annihilate these domains, the algorithm crashes. The exclamation marks indicate (in a general sense) that the DD algorithm has detected something dangerously wrong.
> 
> If you're trying to make drastic changes to the size or dimensions of your system, DD is a bad choice and you'll likely have to use particle decomposition (mdrun -pd).
> 

Or during compression, do regular and frequent grompp -t .trr -e .edr restarts so that the DD information in the checkpoint file is not propagated, and so you can do a new DD based on the current volume.

Mark


> 
> 
> <snip>
> 
> >fourierspacing      =  0.3                 
> 
> You're setting yourself up for inaccurate PME calculations with this.  Use 0.1 - 0.12 unless you've got some compelling reason to decrease your accuracy.
> 
> -Justin
> 
> -- 
> ========================================
> 
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> 
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