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).
<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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