[gmx-users] lincs warning

[Erik Marklund]

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.
> 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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>>
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>
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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
erikm at xray.bmc.uu.se    http://xray.bmc.uu.se/molbiophys