On Jun 3, 2009, at 10:48 AM, Erik Marklund wrote:
XAvier Periole skrev:
On Jun 3, 2009, at 10:01 AM, Ran Friedman wrote:
Hi XAvier,
Do you use virtual sites? I've seen this when I used virtual sites,
No virtual sites.
large time steps and a system that probably wasn't equilibrated
enough.
time step 2 fs and a system totally equilibrated, nothing there.
I would have considered this if the warning were reproduced when
restarting the simulation.
It seems more that it is a loss of accuracy due to communication
between CPUs ?
If you use dynamic load balancing then you are sacrificing binary
reproducibility. Because of this, and the chaotic nature of MD, the
error will likely not occur at the same point in your continuation.
Still, the source of the error persists and is what demands
attention I'd say.
Well starting from a cpt file, I would expect reproducibility at the
difference that the
decomposition over CPUs might be refreshed.
It might be but I am still favoring a communication issue.
I am now testing the effect of using -rdd and -rcon on the LINCS
warnings.
XAvier.
Ran.
XAvier Periole wrote:
Dears,
I am experiencing some problems running a few proteins in water
(GROMOS43a1/SPC)
with gmx-4.0.4 using 32 CPUs.
After some ns lincs warnings appear and eventually the simulation
crashes dues
to too many lincs warnings.
When restarting the simulation feeding "-cpi md.cpt" to mdrun the
simulation restarts
fine and no lincs warning are reported on the same portion of the
simulation. The
simulation runs again for some ns and the same happens: new lincs
warning appear
and eventually the simulation crashes again.
Any explanation for this? Any solution?
Best,
XAvier.
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--
-----------------------------------------------
Erik Marklund, PhD student
Laboratory of Molecular Biophysics,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: +46 18 471 4537 fax: +46 18 511 755
er...@xray.bmc.uu.se http://xray.bmc.uu.se/molbiophys
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