[gmx-users] number of DD cells
Justin A. Lemkul
jalemkul at vt.edu
Fri Mar 4 16:51:53 CET 2011
> 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
> 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
> 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 A. Lemkul
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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